[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/19775410/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/19861013/transformed.cor.cli.txt"

nPatients in clinical file=185, in cluster file=146, common to both=146
[1] "Reduce the number of clustering variables from 198 to 187."
[1] 187 146
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           100             46 
  TP53 MUTATED TP53 WILD-TYPE 
           100             46 
[1] "RBM4 MUTATION ANALYSIS"
[1] 3
  RBM4 MUTATED RBM4 WILD-TYPE 
            62             84 
  RBM4 MUTATED RBM4 WILD-TYPE 
            62             84 
[1] "JMY MUTATION ANALYSIS"
[1] 3
  JMY MUTATED JMY WILD-TYPE 
           55            91 
  JMY MUTATED JMY WILD-TYPE 
           55            91 
[1] "RIOK1 MUTATION ANALYSIS"
[1] 3
  RIOK1 MUTATED RIOK1 WILD-TYPE 
             55              91 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
             55              91 
[1] "LCE2A MUTATION ANALYSIS"
[1] 3
  LCE2A MUTATED LCE2A WILD-TYPE 
             46             100 
  LCE2A MUTATED LCE2A WILD-TYPE 
             46             100 
[1] "C1QB MUTATION ANALYSIS"
[1] 3
  C1QB MUTATED C1QB WILD-TYPE 
            35            111 
  C1QB MUTATED C1QB WILD-TYPE 
            35            111 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             32             114 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             32             114 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              30              116 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              30              116 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            29            117 
  MLL2 MUTATED MLL2 WILD-TYPE 
            29            117 
[1] "AEBP1 MUTATION ANALYSIS"
[1] 3
  AEBP1 MUTATED AEBP1 WILD-TYPE 
             26             120 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
             26             120 
[1] "RBM47 MUTATION ANALYSIS"
[1] 3
  RBM47 MUTATED RBM47 WILD-TYPE 
             25             121 
  RBM47 MUTATED RBM47 WILD-TYPE 
             25             121 
[1] "ANKRD36 MUTATION ANALYSIS"
[1] 3
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               24               122 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               24               122 
[1] "RFX1 MUTATION ANALYSIS"
[1] 3
  RFX1 MUTATED RFX1 WILD-TYPE 
            24            122 
  RFX1 MUTATED RFX1 WILD-TYPE 
            24            122 
[1] "TYRO3 MUTATION ANALYSIS"
[1] 3
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             14             132 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             14             132 
[1] "NCOA3 MUTATION ANALYSIS"
[1] 3
  NCOA3 MUTATED NCOA3 WILD-TYPE 
             14             132 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
             14             132 
[1] "GPR6 MUTATION ANALYSIS"
[1] 3
  GPR6 MUTATED GPR6 WILD-TYPE 
            12            134 
  GPR6 MUTATED GPR6 WILD-TYPE 
            12            134 
[1] "LZTS1 MUTATION ANALYSIS"
[1] 3
  LZTS1 MUTATED LZTS1 WILD-TYPE 
             10             136 
  LZTS1 MUTATED LZTS1 WILD-TYPE 
             10             136 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
           123             23 
  KRAS MUTATED KRAS WILD-TYPE 
           123             23 
[1] "ZMIZ2 MUTATION ANALYSIS"
[1] 3
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
             12             134 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
             12             134 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            16            130 
  IRS4 MUTATED IRS4 WILD-TYPE 
            16            130 
[1] "SIK3 MUTATION ANALYSIS"
[1] 3
  SIK3 MUTATED SIK3 WILD-TYPE 
            13            133 
  SIK3 MUTATED SIK3 WILD-TYPE 
            13            133 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               9              137 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               9              137 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
             5            141 
  RBMX MUTATED RBMX WILD-TYPE 
             5            141 
[1] "ESPN MUTATION ANALYSIS"
[1] 3
  ESPN MUTATED ESPN WILD-TYPE 
             6            140 
  ESPN MUTATED ESPN WILD-TYPE 
             6            140 
[1] "FNDC1 MUTATION ANALYSIS"
[1] 3
  FNDC1 MUTATED FNDC1 WILD-TYPE 
             14             132 
  FNDC1 MUTATED FNDC1 WILD-TYPE 
             14             132 
[1] "ATP2C1 MUTATION ANALYSIS"
[1] 3
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               8              138 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               8              138 
[1] "HACL1 MUTATION ANALYSIS"
[1] 3
  HACL1 MUTATED HACL1 WILD-TYPE 
              5             141 
  HACL1 MUTATED HACL1 WILD-TYPE 
              5             141 
[1] "UBAC1 MUTATION ANALYSIS"
[1] 3
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              5             141 
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              5             141 
[1] "OGFOD1 MUTATION ANALYSIS"
[1] 3
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               5              141 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               5              141 
[1] "CASQ2 MUTATION ANALYSIS"
[1] 3
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              8             138 
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              8             138 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               8              138 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               8              138 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
              9             137 
  RNF43 MUTATED RNF43 WILD-TYPE 
              9             137 
[1] "DCP1B MUTATION ANALYSIS"
[1] 3
  DCP1B MUTATED DCP1B WILD-TYPE 
              9             137 
  DCP1B MUTATED DCP1B WILD-TYPE 
              9             137 
[1] "ZNF678 MUTATION ANALYSIS"
[1] 3
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               5              141 
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               5              141 
[1] "RPL22 MUTATION ANALYSIS"
[1] 3
  RPL22 MUTATED RPL22 WILD-TYPE 
              5             141 
  RPL22 MUTATED RPL22 WILD-TYPE 
              5             141 
[1] "NBPF16 MUTATION ANALYSIS"
[1] 3
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               7              139 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               7              139 
[1] "CD86 MUTATION ANALYSIS"
[1] 3
  CD86 MUTATED CD86 WILD-TYPE 
             6            140 
  CD86 MUTATED CD86 WILD-TYPE 
             6            140 
[1] "PARP10 MUTATION ANALYSIS"
[1] 3
  PARP10 MUTATED PARP10 WILD-TYPE 
               5              141 
  PARP10 MUTATED PARP10 WILD-TYPE 
               5              141 
[1] "VWA3A MUTATION ANALYSIS"
[1] 3
  VWA3A MUTATED VWA3A WILD-TYPE 
              5             141 
  VWA3A MUTATED VWA3A WILD-TYPE 
              5             141 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               11               135 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               11               135 
[1] "PRKRA MUTATION ANALYSIS"
[1] 3
  PRKRA MUTATED PRKRA WILD-TYPE 
              4             142 
  PRKRA MUTATED PRKRA WILD-TYPE 
              4             142 
[1] "RBM12 MUTATION ANALYSIS"
[1] 3
  RBM12 MUTATED RBM12 WILD-TYPE 
              5             141 
  RBM12 MUTATED RBM12 WILD-TYPE 
              5             141 
[1] "ZNF880 MUTATION ANALYSIS"
[1] 3
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               4              142 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               4              142 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              7             139 
  CDC27 MUTATED CDC27 WILD-TYPE 
              7             139 
[1] "SUZ12 MUTATION ANALYSIS"
[1] 3
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              4             142 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              4             142 
[1] "SORBS2 MUTATION ANALYSIS"
[1] 3
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               6              140 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               6              140 
[1] "RNF32 MUTATION ANALYSIS"
[1] 3
  RNF32 MUTATED RNF32 WILD-TYPE 
              5             141 
  RNF32 MUTATED RNF32 WILD-TYPE 
              5             141 
[1] "CBX3 MUTATION ANALYSIS"
[1] 3
  CBX3 MUTATED CBX3 WILD-TYPE 
             4            142 
  CBX3 MUTATED CBX3 WILD-TYPE 
             4            142 
[1] "SDCBP MUTATION ANALYSIS"
[1] 3
  SDCBP MUTATED SDCBP WILD-TYPE 
              6             140 
  SDCBP MUTATED SDCBP WILD-TYPE 
              6             140 
[1] "PLIN4 MUTATION ANALYSIS"
[1] 3
  PLIN4 MUTATED PLIN4 WILD-TYPE 
              7             139 
  PLIN4 MUTATED PLIN4 WILD-TYPE 
              7             139 
[1] "AAK1 MUTATION ANALYSIS"
[1] 3
  AAK1 MUTATED AAK1 WILD-TYPE 
             4            142 
  AAK1 MUTATED AAK1 WILD-TYPE 
             4            142 
[1] "TMCC1 MUTATION ANALYSIS"
[1] 3
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              7             139 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              7             139 
[1] "IYD MUTATION ANALYSIS"
[1] 3
  IYD MUTATED IYD WILD-TYPE 
            6           140 
  IYD MUTATED IYD WILD-TYPE 
            6           140 
[1] "NLRP2 MUTATION ANALYSIS"
[1] 3
  NLRP2 MUTATED NLRP2 WILD-TYPE 
              6             140 
  NLRP2 MUTATED NLRP2 WILD-TYPE 
              6             140 
[1] "SP140 MUTATION ANALYSIS"
[1] 3
  SP140 MUTATED SP140 WILD-TYPE 
              5             141 
  SP140 MUTATED SP140 WILD-TYPE 
              5             141 
[1] "OR2T4 MUTATION ANALYSIS"
[1] 3
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              6             140 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              6             140 
[1] "GPR50 MUTATION ANALYSIS"
[1] 3
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             141 
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             141 
[1] "CFTR MUTATION ANALYSIS"
[1] 3
  CFTR MUTATED CFTR WILD-TYPE 
             7            139 
  CFTR MUTATED CFTR WILD-TYPE 
             7            139 
[1] "GPR98 MUTATION ANALYSIS"
[1] 3
  GPR98 MUTATED GPR98 WILD-TYPE 
              8             138 
  GPR98 MUTATED GPR98 WILD-TYPE 
              8             138 
[1] "DAAM1 MUTATION ANALYSIS"
[1] 3
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              6             140 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              6             140 
[1] "MTBP MUTATION ANALYSIS"
[1] 3
  MTBP MUTATED MTBP WILD-TYPE 
             3            143 
  MTBP MUTATED MTBP WILD-TYPE 
             3            143 
[1] "RREB1 MUTATION ANALYSIS"
[1] 3
  RREB1 MUTATED RREB1 WILD-TYPE 
              9             137 
  RREB1 MUTATED RREB1 WILD-TYPE 
              9             137 
[1] "TRPC4 MUTATION ANALYSIS"
[1] 3
  TRPC4 MUTATED TRPC4 WILD-TYPE 
              6             140 
  TRPC4 MUTATED TRPC4 WILD-TYPE 
              6             140 
[1] "CD2AP MUTATION ANALYSIS"
[1] 3
  CD2AP MUTATED CD2AP WILD-TYPE 
              3             143 
  CD2AP MUTATED CD2AP WILD-TYPE 
              3             143 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
             9            137 
  GNAS MUTATED GNAS WILD-TYPE 
             9            137 
[1] "FAR1 MUTATION ANALYSIS"
[1] 3
  FAR1 MUTATED FAR1 WILD-TYPE 
             4            142 
  FAR1 MUTATED FAR1 WILD-TYPE 
             4            142 
[1] "COL28A1 MUTATION ANALYSIS"
[1] 3
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                5               141 
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                5               141 
[1] "SKA3 MUTATION ANALYSIS"
[1] 3
  SKA3 MUTATED SKA3 WILD-TYPE 
             6            140 
  SKA3 MUTATED SKA3 WILD-TYPE 
             6            140 
[1] "JAK2 MUTATION ANALYSIS"
[1] 3
  JAK2 MUTATED JAK2 WILD-TYPE 
             4            142 
  JAK2 MUTATED JAK2 WILD-TYPE 
             4            142 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               7              139 
  ARID1A MUTATED ARID1A WILD-TYPE 
               7              139 
[1] "KCNA7 MUTATION ANALYSIS"
[1] 3
  KCNA7 MUTATED KCNA7 WILD-TYPE 
              5             141 
  KCNA7 MUTATED KCNA7 WILD-TYPE 
              5             141 
[1] "CHRNA9 MUTATION ANALYSIS"
[1] 3
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               4              142 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               4              142 
[1] "KLHL20 MUTATION ANALYSIS"
[1] 3
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               3              143 
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               3              143 
[1] "NUP210L MUTATION ANALYSIS"
[1] 3
  NUP210L MUTATED NUP210L WILD-TYPE 
                5               141 
  NUP210L MUTATED NUP210L WILD-TYPE 
                5               141 
[1] "AQP7 MUTATION ANALYSIS"
[1] 3
  AQP7 MUTATED AQP7 WILD-TYPE 
             6            140 
  AQP7 MUTATED AQP7 WILD-TYPE 
             6            140 
[1] "P2RY1 MUTATION ANALYSIS"
[1] 3
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              5             141 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              5             141 
[1] "CCDC33 MUTATION ANALYSIS"
[1] 3
  CCDC33 MUTATED CCDC33 WILD-TYPE 
               3              143 
  CCDC33 MUTATED CCDC33 WILD-TYPE 
               3              143 
[1] "WRN MUTATION ANALYSIS"
[1] 3
  WRN MUTATED WRN WILD-TYPE 
            4           142 
  WRN MUTATED WRN WILD-TYPE 
            4           142 
[1] "C1ORF125 MUTATION ANALYSIS"
[1] 3
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
                 4                142 
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
                 4                142 
[1] "SIGLEC14 MUTATION ANALYSIS"
[1] 3
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 4                142 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 4                142 
[1] "KRT2 MUTATION ANALYSIS"
[1] 3
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            141 
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            141 
[1] "MSH2 MUTATION ANALYSIS"
[1] 3
  MSH2 MUTATED MSH2 WILD-TYPE 
             4            142 
  MSH2 MUTATED MSH2 WILD-TYPE 
             4            142 
[1] "MORF4L1 MUTATION ANALYSIS"
[1] 3
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                3               143 
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                3               143 
[1] "KIAA0586 MUTATION ANALYSIS"
[1] 3
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 6                140 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 6                140 
[1] "SYT14 MUTATION ANALYSIS"
[1] 3
  SYT14 MUTATED SYT14 WILD-TYPE 
              4             142 
  SYT14 MUTATED SYT14 WILD-TYPE 
              4             142 
[1] "TAX1BP1 MUTATION ANALYSIS"
[1] 3
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                5               141 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                5               141 
[1] "HSPE1 MUTATION ANALYSIS"
[1] 3
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              4             142 
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              4             142 
[1] "GPSM2 MUTATION ANALYSIS"
[1] 3
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3             143 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3             143 
[1] "HELZ MUTATION ANALYSIS"
[1] 3
  HELZ MUTATED HELZ WILD-TYPE 
             5            141 
  HELZ MUTATED HELZ WILD-TYPE 
             5            141 
[1] "DOCK8 MUTATION ANALYSIS"
[1] 3
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              5             141 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              5             141 
[1] "COBL MUTATION ANALYSIS"
[1] 3
  COBL MUTATED COBL WILD-TYPE 
             6            140 
  COBL MUTATED COBL WILD-TYPE 
             6            140 
[1] "GSN MUTATION ANALYSIS"
[1] 3
  GSN MUTATED GSN WILD-TYPE 
            4           142 
  GSN MUTATED GSN WILD-TYPE 
            4           142 
[1] "NAA20 MUTATION ANALYSIS"
[1] 3
  NAA20 MUTATED NAA20 WILD-TYPE 
              3             143 
  NAA20 MUTATED NAA20 WILD-TYPE 
              3             143 
[1] "ZACN MUTATION ANALYSIS"
[1] 3
  ZACN MUTATED ZACN WILD-TYPE 
             3            143 
  ZACN MUTATED ZACN WILD-TYPE 
             3            143 
[1] "AP3B1 MUTATION ANALYSIS"
[1] 3
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              4             142 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              4             142 
[1] "C3ORF15 MUTATION ANALYSIS"
[1] 3
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
                5               141 
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
                5               141 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               7              139 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               7              139 
[1] "RBL2 MUTATION ANALYSIS"
[1] 3
  RBL2 MUTATED RBL2 WILD-TYPE 
             4            142 
  RBL2 MUTATED RBL2 WILD-TYPE 
             4            142 
[1] "OMA1 MUTATION ANALYSIS"
[1] 3
  OMA1 MUTATED OMA1 WILD-TYPE 
             3            143 
  OMA1 MUTATED OMA1 WILD-TYPE 
             3            143 
[1] "SORT1 MUTATION ANALYSIS"
[1] 3
  SORT1 MUTATED SORT1 WILD-TYPE 
              5             141 
  SORT1 MUTATED SORT1 WILD-TYPE 
              5             141 
[1] "NBPF9 MUTATION ANALYSIS"
[1] 3
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              3             143 
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              3             143 
[1] "C5ORF51 MUTATION ANALYSIS"
[1] 3
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                3               143 
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                3               143 
[1] "CSTF2T MUTATION ANALYSIS"
[1] 3
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               3              143 
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               3              143 
[1] "SSBP3 MUTATION ANALYSIS"
[1] 3
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             143 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             143 
[1] "PRSS3 MUTATION ANALYSIS"
[1] 3
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              3             143 
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              3             143 
[1] "UBXN4 MUTATION ANALYSIS"
[1] 3
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              3             143 
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              3             143 
[1] "AGAP6 MUTATION ANALYSIS"
[1] 3
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              7             139 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              7             139 
[1] "TGM5 MUTATION ANALYSIS"
[1] 3
  TGM5 MUTATED TGM5 WILD-TYPE 
             4            142 
  TGM5 MUTATED TGM5 WILD-TYPE 
             4            142 
[1] "GPRC6A MUTATION ANALYSIS"
[1] 3
  GPRC6A MUTATED GPRC6A WILD-TYPE 
               5              141 
  GPRC6A MUTATED GPRC6A WILD-TYPE 
               5              141 
[1] "OR52D1 MUTATION ANALYSIS"
[1] 3
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               4              142 
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               4              142 
[1] "KLK13 MUTATION ANALYSIS"
[1] 3
  KLK13 MUTATED KLK13 WILD-TYPE 
              5             141 
  KLK13 MUTATED KLK13 WILD-TYPE 
              5             141 
[1] "BRD8 MUTATION ANALYSIS"
[1] 3
  BRD8 MUTATED BRD8 WILD-TYPE 
             3            143 
  BRD8 MUTATED BRD8 WILD-TYPE 
             3            143 
[1] "ZMYM2 MUTATION ANALYSIS"
[1] 3
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              3             143 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              3             143 
[1] "ZNF780A MUTATION ANALYSIS"
[1] 3
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                5               141 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                5               141 
[1] "MLPH MUTATION ANALYSIS"
[1] 3
  MLPH MUTATED MLPH WILD-TYPE 
             3            143 
  MLPH MUTATED MLPH WILD-TYPE 
             3            143 
[1] "NLRP6 MUTATION ANALYSIS"
[1] 3
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             143 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             143 
[1] "SEPT2 MUTATION ANALYSIS"
[1] 3
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              3             143 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              3             143 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
              3             143 
  MMP13 MUTATED MMP13 WILD-TYPE 
              3             143 
[1] "OXR1 MUTATION ANALYSIS"
[1] 3
  OXR1 MUTATED OXR1 WILD-TYPE 
             3            143 
  OXR1 MUTATED OXR1 WILD-TYPE 
             3            143 
[1] "LACTB MUTATION ANALYSIS"
[1] 3
  LACTB MUTATED LACTB WILD-TYPE 
              3             143 
  LACTB MUTATED LACTB WILD-TYPE 
              3             143 
[1] "SYCP2 MUTATION ANALYSIS"
[1] 3
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              5             141 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              5             141 
[1] "WDHD1 MUTATION ANALYSIS"
[1] 3
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              3             143 
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              3             143 
[1] "RTTN MUTATION ANALYSIS"
[1] 3
  RTTN MUTATED RTTN WILD-TYPE 
             5            141 
  RTTN MUTATED RTTN WILD-TYPE 
             5            141 
[1] "TDRD5 MUTATION ANALYSIS"
[1] 3
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              4             142 
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              4             142 
[1] "SEPHS2 MUTATION ANALYSIS"
[1] 3
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               5              141 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               5              141 
[1] "ACTRT2 MUTATION ANALYSIS"
[1] 3
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               3              143 
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               3              143 
[1] "DNAH7 MUTATION ANALYSIS"
[1] 3
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              7             139 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              7             139 
[1] "MC3R MUTATION ANALYSIS"
[1] 3
  MC3R MUTATED MC3R WILD-TYPE 
             4            142 
  MC3R MUTATED MC3R WILD-TYPE 
             4            142 
[1] "FAM8A1 MUTATION ANALYSIS"
[1] 3
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               4              142 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               4              142 
[1] "TGFBR1 MUTATION ANALYSIS"
[1] 3
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               8              138 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               8              138 
[1] "L1CAM MUTATION ANALYSIS"
[1] 3
  L1CAM MUTATED L1CAM WILD-TYPE 
              6             140 
  L1CAM MUTATED L1CAM WILD-TYPE 
              6             140 
[1] "LCP2 MUTATION ANALYSIS"
[1] 3
  LCP2 MUTATED LCP2 WILD-TYPE 
             3            143 
  LCP2 MUTATED LCP2 WILD-TYPE 
             3            143 
[1] "ZNF358 MUTATION ANALYSIS"
[1] 3
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               4              142 
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               4              142 
[1] "KCNE1 MUTATION ANALYSIS"
[1] 3
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              4             142 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              4             142 
[1] "OR1N2 MUTATION ANALYSIS"
[1] 3
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              5             141 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              5             141 
[1] "FLVCR1 MUTATION ANALYSIS"
[1] 3
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               3              143 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               3              143 
[1] "BTN2A1 MUTATION ANALYSIS"
[1] 3
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               3              143 
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               3              143 
[1] "PAPSS2 MUTATION ANALYSIS"
[1] 3
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               4              142 
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               4              142 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              5             141 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              5             141 
[1] "CYTH4 MUTATION ANALYSIS"
[1] 3
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              3             143 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              3             143 
[1] "ANKRD49 MUTATION ANALYSIS"
[1] 3
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3               143 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3               143 
[1] "CMYA5 MUTATION ANALYSIS"
[1] 3
  CMYA5 MUTATED CMYA5 WILD-TYPE 
              8             138 
  CMYA5 MUTATED CMYA5 WILD-TYPE 
              8             138 
[1] "PHF15 MUTATION ANALYSIS"
[1] 3
  PHF15 MUTATED PHF15 WILD-TYPE 
              4             142 
  PHF15 MUTATED PHF15 WILD-TYPE 
              4             142 
[1] "RSPO1 MUTATION ANALYSIS"
[1] 3
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              3             143 
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              3             143 
[1] "ASH1L MUTATION ANALYSIS"
[1] 3
  ASH1L MUTATED ASH1L WILD-TYPE 
              6             140 
  ASH1L MUTATED ASH1L WILD-TYPE 
              6             140 
[1] "BVES MUTATION ANALYSIS"
[1] 3
  BVES MUTATED BVES WILD-TYPE 
             4            142 
  BVES MUTATED BVES WILD-TYPE 
             4            142 
[1] "DDX4 MUTATION ANALYSIS"
[1] 3
  DDX4 MUTATED DDX4 WILD-TYPE 
             5            141 
  DDX4 MUTATED DDX4 WILD-TYPE 
             5            141 
[1] "TEKT4 MUTATION ANALYSIS"
[1] 3
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              6             140 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              6             140 
[1] "WWP2 MUTATION ANALYSIS"
[1] 3
  WWP2 MUTATED WWP2 WILD-TYPE 
             5            141 
  WWP2 MUTATED WWP2 WILD-TYPE 
             5            141 
[1] "DHX35 MUTATION ANALYSIS"
[1] 3
  DHX35 MUTATED DHX35 WILD-TYPE 
              4             142 
  DHX35 MUTATED DHX35 WILD-TYPE 
              4             142 
[1] "WDR36 MUTATION ANALYSIS"
[1] 3
  WDR36 MUTATED WDR36 WILD-TYPE 
              3             143 
  WDR36 MUTATED WDR36 WILD-TYPE 
              3             143 
[1] "DRD1 MUTATION ANALYSIS"
[1] 3
  DRD1 MUTATED DRD1 WILD-TYPE 
             4            142 
  DRD1 MUTATED DRD1 WILD-TYPE 
             4            142 
[1] "ENTPD2 MUTATION ANALYSIS"
[1] 3
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               4              142 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               4              142 
[1] "SRFBP1 MUTATION ANALYSIS"
[1] 3
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3              143 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3              143 
[1] "CSRNP3 MUTATION ANALYSIS"
[1] 3
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               4              142 
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               4              142 
[1] "REXO1 MUTATION ANALYSIS"
[1] 3
  REXO1 MUTATED REXO1 WILD-TYPE 
              3             143 
  REXO1 MUTATED REXO1 WILD-TYPE 
              3             143 
[1] "CEACAM4 MUTATION ANALYSIS"
[1] 3
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                4               142 
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                4               142 
[1] "SARS2 MUTATION ANALYSIS"
[1] 3
  SARS2 MUTATED SARS2 WILD-TYPE 
              3             143 
  SARS2 MUTATED SARS2 WILD-TYPE 
              3             143 
[1] "CPNE2 MUTATION ANALYSIS"
[1] 3
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              3             143 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              3             143 
[1] "CYTSA MUTATION ANALYSIS"
[1] 3
  CYTSA MUTATED CYTSA WILD-TYPE 
              4             142 
  CYTSA MUTATED CYTSA WILD-TYPE 
              4             142 
[1] "LUZP1 MUTATION ANALYSIS"
[1] 3
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              4             142 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              4             142 
[1] "CCDC87 MUTATION ANALYSIS"
[1] 3
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               3              143 
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               3              143 
[1] "ZBTB4 MUTATION ANALYSIS"
[1] 3
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              4             142 
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              4             142 
[1] "MLL5 MUTATION ANALYSIS"
[1] 3
  MLL5 MUTATED MLL5 WILD-TYPE 
             4            142 
  MLL5 MUTATED MLL5 WILD-TYPE 
             4            142 
[1] "ADORA3 MUTATION ANALYSIS"
[1] 3
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               5              141 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               5              141 
[1] "ARHGAP9 MUTATION ANALYSIS"
[1] 3
  ARHGAP9 MUTATED ARHGAP9 WILD-TYPE 
                4               142 
  ARHGAP9 MUTATED ARHGAP9 WILD-TYPE 
                4               142 
[1] "ANKRD30A MUTATION ANALYSIS"
[1] 3
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 8                138 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 8                138 
[1] "KIF4B MUTATION ANALYSIS"
[1] 3
  KIF4B MUTATED KIF4B WILD-TYPE 
              5             141 
  KIF4B MUTATED KIF4B WILD-TYPE 
              5             141 
[1] "ATP2C2 MUTATION ANALYSIS"
[1] 3
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               4              142 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               4              142 
[1] "POM121 MUTATION ANALYSIS"
[1] 3
  POM121 MUTATED POM121 WILD-TYPE 
               5              141 
  POM121 MUTATED POM121 WILD-TYPE 
               5              141 
[1] "DDB1 MUTATION ANALYSIS"
[1] 3
  DDB1 MUTATED DDB1 WILD-TYPE 
             5            141 
  DDB1 MUTATED DDB1 WILD-TYPE 
             5            141 
[1] "NUP54 MUTATION ANALYSIS"
[1] 3
  NUP54 MUTATED NUP54 WILD-TYPE 
              3             143 
  NUP54 MUTATED NUP54 WILD-TYPE 
              3             143 
[1] "C14ORF21 MUTATION ANALYSIS"
[1] 3
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 4                142 
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 4                142 
[1] "LILRB2 MUTATION ANALYSIS"
[1] 3
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               4              142 
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               4              142 
[1] "ADAMTSL4 MUTATION ANALYSIS"
[1] 3
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                 5                141 
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                 5                141 
[1] "ZNF483 MUTATION ANALYSIS"
[1] 3
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               4              142 
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               4              142 
[1] "ANKRD28 MUTATION ANALYSIS"
[1] 3
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
                6               140 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
                6               140 
[1] "DIO1 MUTATION ANALYSIS"
[1] 3
  DIO1 MUTATED DIO1 WILD-TYPE 
             4            142 
  DIO1 MUTATED DIO1 WILD-TYPE 
             4            142 
[1] "KLK15 MUTATION ANALYSIS"
[1] 3
  KLK15 MUTATED KLK15 WILD-TYPE 
              5             141 
  KLK15 MUTATED KLK15 WILD-TYPE 
              5             141 
[1] "BOC MUTATION ANALYSIS"
[1] 3
  BOC MUTATED BOC WILD-TYPE 
            4           142 
  BOC MUTATED BOC WILD-TYPE 
            4           142 
[1] "NDUFV2 MUTATION ANALYSIS"
[1] 3
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              143 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              143 
[1] "MAP3K9 MUTATION ANALYSIS"
[1] 3
  MAP3K9 MUTATED MAP3K9 WILD-TYPE 
               5              141 
  MAP3K9 MUTATED MAP3K9 WILD-TYPE 
               5              141 
[1] "TNRC6C MUTATION ANALYSIS"
[1] 3
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               6              140 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               6              140 
[1] "PDXDC1 MUTATION ANALYSIS"
[1] 3
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               3              143 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               3              143 
[1] "MIPEP MUTATION ANALYSIS"
[1] 3
  MIPEP MUTATED MIPEP WILD-TYPE 
              3             143 
  MIPEP MUTATED MIPEP WILD-TYPE 
              3             143 
[1] "ENPP7 MUTATION ANALYSIS"
[1] 3
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              5             141 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              5             141 
[1] "FCGBP MUTATION ANALYSIS"
[1] 3
  FCGBP MUTATED FCGBP WILD-TYPE 
             12             134 
  FCGBP MUTATED FCGBP WILD-TYPE 
             12             134 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "NUMBER_PACK_YEARS_SMOKED"            
[15] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 146 columns.

[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=72,	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=89,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "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 146 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "RESIDUAL_TUMOR"                "NUMBER_OF_LYMPH_NODES"        
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=44, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
  4  16 122   3 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    4    16   125 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  4  16 122   3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    4    16   125 
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
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=29, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=28, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, 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 = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   44 55
  TP53 WILD-TYPE 24 21
  TP53 MUTATED TP53 WILD-TYPE 
            99             45 
  TP53 MUTATED TP53 WILD-TYPE 
            55             21 
$`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 
       42.31        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        33.57        15.06        10.13        24.43 
TCGA-F2-6879 TCGA-F2-A7TX TCGA-F2-A8YN TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPS 
       10.98         3.12        17.00        12.66         0.03         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-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
        4.21         9.50        66.94         8.28        30.25        17.49 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
        0.13        20.19        23.21        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08        19.82        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-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-A7M4 TCGA-IB-AAUN 
       15.12        20.88        21.90         1.35        15.88         4.73 
TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUS TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A9Q5 
       14.17         6.02         7.40         8.05        12.92        10.29 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-RB-AA9M TCGA-S4-A8RO TCGA-US-A774 
       19.20         8.78        15.45         9.40        17.26        22.85 
TCGA-US-A779 TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
       16.80        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-Z5-AAPL 
       23.67        12.76        15.35 

$`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        58.98        43.50        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        16.37 
TCGA-FB-AAPU TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-HV-A5A4 TCGA-HZ-7919 TCGA-HZ-7926 
       12.53         4.04         1.02         7.63        19.50        17.03 
TCGA-HZ-8002 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-A49H TCGA-HZ-A8P1 TCGA-IB-7651 
       12.03        12.43        14.93        16.14         0.23        19.82 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SQ TCGA-IB-A7LX 
       41.33        21.30        15.98         2.47         7.20         8.22 
TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUR TCGA-IB-AAUT TCGA-LB-A8F3 TCGA-Q3-A5QY 
        0.26         7.86        11.11         9.44        12.46        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A77E 
        3.12        15.32        24.23        23.08        39.98        14.14 
TCGA-US-A77G TCGA-YB-A89D TCGA-YY-A8LH 
        0.39        11.51        66.28 

  TP53 MUTATED TP53 WILD-TYPE 
          0.03           0.23 
  TP53 MUTATED TP53 WILD-TYPE 
         66.94          75.12 
  TP53 MUTATED TP53 WILD-TYPE 
         14.40          14.14 
[1] "0.0 - 66.9 (14.4)" "0.2 - 75.1 (14.1)"
[1] "hr=" "1.4"
D1V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TP53 MUTATED          1        4        16        72         3        4
  TP53 WILD-TYPE        2        4         7        31         1        0
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE IA             1              2
  STAGE IB             4              4
  STAGE IIA           16              7
  STAGE IIB           72             31
  STAGE III            3              1
  STAGE IV             4              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 11    87
  TP53 WILD-TYPE  2  5    38
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1               2              2
  T2              11              5
  T3+T4           87             38
[1] 3 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
  TP53 MUTATED   24 75
  TP53 WILD-TYPE 13 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     24   75
  TP53 WILD-TYPE   13   33
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           24             13
  1           75             33
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus              0  1
  TP53 MUTATED   50  4
  TP53 WILD-TYPE 16  0
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     50    4
  TP53 WILD-TYPE   16    0
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           50             16
  1            4              0
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus              0  1
  TP53 MUTATED   47 53
  TP53 WILD-TYPE 20 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     47   53
  TP53 WILD-TYPE   20   26
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           47             20
  MALE             53             26
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus              0  1
  TP53 MUTATED   68 23
  TP53 WILD-TYPE 26 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     68   23
  TP53 WILD-TYPE   26   13
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            68             26
  YES           23             13
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TP53 MUTATED                                    89
  TP53 WILD-TYPE                                  41
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TP53 MUTATED                                      10
  TP53 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TP53 MUTATED                                                  0
  TP53 WILD-TYPE                                                2
D1V9, multiclass
                                                  clus
vv                                                 TP53 MUTATED TP53 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        89             41
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      10              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"
D1V10, continuous
D1V11, continuous
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   50 39  4  1
  TP53 WILD-TYPE 29 11  0  2
D1V12, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           50             29
  R1           39             11
  R2            4              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"
D1V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       7                         2    87
  TP53 WILD-TYPE     2                         3    41
D1V14, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                7              2
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                               87             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"
D1V15, binary
                cls
clus              0  1
  TP53 MUTATED    4 64
  TP53 WILD-TYPE  1 41
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4   64
  TP53 WILD-TYPE    1   41
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                4              1
  NOT HISPANIC OR LATINO           64             41
[1] 2 2
[1] FALSE

Clustering(2) Variable = RBM4 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  RBM4 MUTATED   25 36
  RBM4 WILD-TYPE 43 40
  RBM4 MUTATED RBM4 WILD-TYPE 
            61             83 
  RBM4 MUTATED RBM4 WILD-TYPE 
            36             40 
$`RBM4 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABA TCGA-2J-AABK TCGA-2J-AABO 
       23.97         9.63         2.63        19.96        15.91        14.47 
TCGA-2J-AABV TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IU 
       21.44        12.95         9.60         7.36        24.26        15.06 
TCGA-3A-A9IZ TCGA-F2-6879 TCGA-F2-A7TX TCGA-FB-A4P6 TCGA-FB-A545 TCGA-FB-A5VM 
       10.13        10.98         3.12        11.93        12.66        16.37 
TCGA-FB-AAPU TCGA-FB-AAQ0 TCGA-FB-AAQ3 TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 
       12.53        15.55         1.02         4.21         7.63        66.94 
TCGA-HV-A7OL TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-8315 
        8.28        20.19        23.21        12.03         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A8P1 
       12.43        14.93        16.14        21.60         5.26         0.23 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7652 
       19.82        12.95        49.38         4.77        15.35        23.80 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8127 TCGA-IB-A5SO 
        3.62        43.79        21.30        15.98        17.16        12.00 
TCGA-IB-AAUM TCGA-IB-AAUO TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-S4-A8RO 
        0.26         7.86        12.46        19.20        15.45        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-XD-AAUL TCGA-XN-A8T5 
       23.08        22.85        39.98        14.14        16.37        23.67 
TCGA-YB-A89D 
       11.51 

$`RBM4 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB9 TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH TCGA-2J-AABR 
        2.17        20.61        22.22        22.72        42.31        14.40 
TCGA-2J-AABU TCGA-2L-AAQA TCGA-2L-AAQE TCGA-2L-AAQI TCGA-3A-A9I5 TCGA-3A-A9I7 
        9.11         4.70        22.49         3.39        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       20.84        33.57        34.09        24.43        75.12        71.74 
TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A8YN TCGA-FB-A4P5 TCGA-FB-A78T TCGA-FB-AAPS 
        7.66        19.27        17.00         5.88         0.03         7.50 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-H6-A45N 
       34.82        23.54         4.04         5.03        12.89        13.84 
TCGA-HV-A5A5 TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        9.50        30.25        17.49        19.50         0.13        17.03 
TCGA-HZ-8003 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A77P 
       19.59        17.92        21.70        10.13         6.38        10.85 
TCGA-HZ-A77Q TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7889 
        1.08        21.90        19.82        41.33         4.04        15.81 
TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
       19.66         3.85         2.47        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-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-A9Q5 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.92        10.29         8.78        13.68         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RM TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
        9.40        24.23        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.03        31.27        12.76        66.28        15.35 

  RBM4 MUTATED RBM4 WILD-TYPE 
          0.23           0.03 
  RBM4 MUTATED RBM4 WILD-TYPE 
         66.94          75.12 
  RBM4 MUTATED RBM4 WILD-TYPE 
         14.47          14.17 
[1] "0.2 - 66.9 (14.5)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.3"
D2V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RBM4 MUTATED          1        3        12        42         2        2
  RBM4 WILD-TYPE        2        5        11        61         2        2
D2V3, multiclass
           clus
vv          RBM4 MUTATED RBM4 WILD-TYPE
  STAGE IA             1              2
  STAGE IB             3              5
  STAGE IIA           12             11
  STAGE IIB           42             61
  STAGE III            2              2
  STAGE IV             2              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
  RBM4 MUTATED    1  6    55
  RBM4 WILD-TYPE  3 10    70
D2V4, multiclass
       clus
vv      RBM4 MUTATED RBM4 WILD-TYPE
  T1               1              3
  T2               6             10
  T3+T4           55             70
[1] 3 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
  RBM4 MUTATED   18 43
  RBM4 WILD-TYPE 19 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM4 MUTATED     18   43
  RBM4 WILD-TYPE   19   65
   clus
vv  RBM4 MUTATED RBM4 WILD-TYPE
  0           18             19
  1           43             65
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus              0  1
  RBM4 MUTATED   26  2
  RBM4 WILD-TYPE 40  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM4 MUTATED     26    2
  RBM4 WILD-TYPE   40    2
   clus
vv  RBM4 MUTATED RBM4 WILD-TYPE
  0           26             40
  1            2              2
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus              0  1
  RBM4 MUTATED   28 34
  RBM4 WILD-TYPE 39 45
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM4 MUTATED     28   34
  RBM4 WILD-TYPE   39   45
        clus
vv       RBM4 MUTATED RBM4 WILD-TYPE
  FEMALE           28             39
  MALE             34             45
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus              0  1
  RBM4 MUTATED   43 15
  RBM4 WILD-TYPE 51 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM4 MUTATED     43   15
  RBM4 WILD-TYPE   51   21
     clus
vv    RBM4 MUTATED RBM4 WILD-TYPE
  NO            43             51
  YES           15             21
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM4 MUTATED                                    54
  RBM4 WILD-TYPE                                  76
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM4 MUTATED                                       7
  RBM4 WILD-TYPE                                     6
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM4 MUTATED                                                  1
  RBM4 WILD-TYPE                                                1
D2V9, multiclass
                                                  clus
vv                                                 RBM4 MUTATED RBM4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        54             76
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       7              6
  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"
D2V10, continuous
D2V11, continuous
                vv
clus             R0 R1 R2 RX
  RBM4 MUTATED   32 23  1  1
  RBM4 WILD-TYPE 47 27  3  2
D2V12, multiclass
    clus
vv   RBM4 MUTATED RBM4 WILD-TYPE
  R0           32             47
  R1           23             27
  R2            1              3
  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"
D2V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM4 MUTATED       6                         2    51
  RBM4 WILD-TYPE     3                         3    77
D2V14, multiclass
                           clus
vv                          RBM4 MUTATED RBM4 WILD-TYPE
  ASIAN                                6              3
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                               51             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"
D2V15, binary
                cls
clus              0  1
  RBM4 MUTATED    2 40
  RBM4 WILD-TYPE  3 65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM4 MUTATED      2   40
  RBM4 WILD-TYPE    3   65
                        clus
vv                       RBM4 MUTATED RBM4 WILD-TYPE
  HISPANIC OR LATINO                2              3
  NOT HISPANIC OR LATINO           40             65
[1] 2 2
[1] FALSE

Clustering(3) Variable = JMY MUTATION ANALYSIS
D3V1, survival
               sevent
clus2            0  1
  JMY MUTATED   28 27
  JMY WILD-TYPE 40 49
  JMY MUTATED JMY WILD-TYPE 
           55            89 
  JMY MUTATED JMY WILD-TYPE 
           27            49 
$`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        24.43 
TCGA-F2-6879 TCGA-F2-A44H TCGA-FB-A545 TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY 
       10.98        19.27        12.66         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-AA8V TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
        4.21         7.63        30.25         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
       23.21         9.83        17.92        21.70        16.14         6.38 
TCGA-HZ-A77O TCGA-HZ-A8P1 TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
        5.26         0.23         4.77        15.35        19.82        23.80 
TCGA-IB-7887 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A6UG 
        3.62         2.47        17.16        12.00        15.85         1.35 
TCGA-IB-A7M4 TCGA-IB-AAUU TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-S4-A8RM 
       15.88         8.05        19.20         8.78        13.68        24.23 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T5 
       16.80        14.14         0.39        12.99        12.03        23.67 
TCGA-YH-A8SY 
       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        42.31 
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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3E-AAAY 
       20.84        24.26        33.57        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-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       16.37         7.50         1.02         9.50        66.94         8.28 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 
       17.49        19.50        12.03        19.59         3.95        12.43 
TCGA-HZ-8519 TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A9TJ 
       14.93        10.13        21.60        10.85         1.08        19.82 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 
       12.95        49.38        21.90        41.33         4.04        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-A5SQ 
       15.81        19.66        21.30         3.85        15.98         7.20 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-AAUM TCGA-IB-AAUN 
       15.12        20.88        21.90         8.22         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-LB-A9Q5 TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 
       12.92        12.46        10.29        15.45         3.12        15.32 
TCGA-RB-AA9M TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-XD-AAUG 
        9.40        17.26        23.08        22.85        39.98        13.81 
TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       16.37        31.27        11.51        66.28        15.35 

  JMY MUTATED JMY WILD-TYPE 
         0.03          0.26 
  JMY MUTATED JMY WILD-TYPE 
        34.82         75.12 
  JMY MUTATED JMY WILD-TYPE 
        13.68         14.93 
[1] "0.0 - 34.8 (13.7)" "0.3 - 75.1 (14.9)"
[1] "hr=" "1.1"
D3V2, continuous
               vv
clus            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  JMY MUTATED          0        2        10        39         3        1
  JMY WILD-TYPE        3        6        13        64         1        3
D3V3, multiclass
           clus
vv          JMY MUTATED JMY WILD-TYPE
  STAGE IA            0             3
  STAGE IB            2             6
  STAGE IIA          10            13
  STAGE IIB          39            64
  STAGE III           3             1
  STAGE IV            1             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
  JMY MUTATED    0  7    48
  JMY WILD-TYPE  4  9    77
D3V4, multiclass
       clus
vv      JMY MUTATED JMY WILD-TYPE
  T1              0             4
  T2              7             9
  T3+T4          48            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"
D3V5, binary
               cls
clus             0  1
  JMY MUTATED   13 41
  JMY WILD-TYPE 24 67
[1] "tbl2"
               cls
clus            [,1] [,2]
  JMY MUTATED     13   41
  JMY WILD-TYPE   24   67
   clus
vv  JMY MUTATED JMY WILD-TYPE
  0          13            24
  1          41            67
[1] 2 2
[1] FALSE
D3V6, binary
               cls
clus             0  1
  JMY MUTATED   23  1
  JMY WILD-TYPE 43  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  JMY MUTATED     23    1
  JMY WILD-TYPE   43    3
   clus
vv  JMY MUTATED JMY WILD-TYPE
  0          23            43
  1           1             3
[1] 2 2
[1] FALSE
D3V7, binary
               cls
clus             0  1
  JMY MUTATED   25 30
  JMY WILD-TYPE 42 49
[1] "tbl2"
               cls
clus            [,1] [,2]
  JMY MUTATED     25   30
  JMY WILD-TYPE   42   49
        clus
vv       JMY MUTATED JMY WILD-TYPE
  FEMALE          25            42
  MALE            30            49
[1] 2 2
[1] FALSE
D3V8, binary
               cls
clus             0  1
  JMY MUTATED   35 11
  JMY WILD-TYPE 59 25
[1] "tbl2"
               cls
clus            [,1] [,2]
  JMY MUTATED     35   11
  JMY WILD-TYPE   59   25
     clus
vv    JMY MUTATED JMY WILD-TYPE
  NO           35            59
  YES          11            25
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  JMY MUTATED                                    49
  JMY WILD-TYPE                                  81
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  JMY MUTATED                                       5
  JMY WILD-TYPE                                     8
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  JMY MUTATED                                                  0
  JMY WILD-TYPE                                                2
D3V9, multiclass
                                                  clus
vv                                                 JMY MUTATED JMY WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       49            81
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      5             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"
D3V10, continuous
D3V11, continuous
               vv
clus            R0 R1 R2 RX
  JMY MUTATED   26 21  2  1
  JMY WILD-TYPE 53 29  2  2
D3V12, multiclass
    clus
vv   JMY MUTATED JMY WILD-TYPE
  R0          26            53
  R1          21            29
  R2           2             2
  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"
D3V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  JMY MUTATED       5                         1    47
  JMY WILD-TYPE     4                         4    81
D3V14, multiclass
                           clus
vv                          JMY MUTATED JMY WILD-TYPE
  ASIAN                               5             4
  BLACK OR AFRICAN AMERICAN           1             4
  WHITE                              47            81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
               cls
clus             0  1
  JMY MUTATED    2 41
  JMY WILD-TYPE  3 64
[1] "tbl2"
               cls
clus            [,1] [,2]
  JMY MUTATED      2   41
  JMY WILD-TYPE    3   64
                        clus
vv                       JMY MUTATED JMY WILD-TYPE
  HISPANIC OR LATINO               2             3
  NOT HISPANIC OR LATINO          41            64
[1] 2 2
[1] FALSE

Clustering(4) Variable = RIOK1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  RIOK1 MUTATED   27 27
  RIOK1 WILD-TYPE 41 49
  RIOK1 MUTATED RIOK1 WILD-TYPE 
             54              90 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
             27              49 
$`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        33.57        15.06        75.12         5.88 
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPZ TCGA-H6-A45N 
       12.66        16.37         0.03        12.53        23.54        13.84 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HZ-7922 TCGA-HZ-8003 
        7.63         9.50        66.94         8.28         0.13        19.59 
TCGA-HZ-8317 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7644 
       12.43        21.70         6.38         5.26        10.85        12.95 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7888 
        4.77        21.90        15.35        19.82        41.33        43.79 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-AAUO TCGA-IB-AAUQ 
       19.66        21.30         2.47        17.16         7.86         6.02 
TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-AA2A 
        9.44         8.05        10.29        19.20        15.45         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-US-A776 TCGA-US-A779 TCGA-XN-A8T3 TCGA-Z5-AAPL 
       15.32         9.40        39.98        16.80        31.27        15.35 

$`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 
       42.31        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 
       58.98        43.50        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 
       24.43        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-HV-A5A3 TCGA-HV-AA8V TCGA-HV-AA8X 
        5.03         1.02        12.89         4.21        30.25        17.49 
TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8005 
       19.50        20.19        17.03        23.21        12.03         3.95 
TCGA-HZ-8315 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK 
        9.83        14.93        17.92        16.14        10.13        21.60 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7652 TCGA-IB-7886 
        1.08         0.23        19.82        49.38        23.80         4.04 
TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-A5SO TCGA-IB-A5SP 
        3.62        15.81         3.85        15.98        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-AAUR TCGA-IB-AAUS 
       15.88         0.26         4.73        14.17        11.11         7.40 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-S4-A8RM TCGA-S4-A8RO 
       12.92        12.46         8.78        13.68        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       23.08        22.85        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        16.37        23.67        11.51        12.76        66.28 

  RIOK1 MUTATED RIOK1 WILD-TYPE 
           0.03            0.23 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
          75.12           71.74 
  RIOK1 MUTATED RIOK1 WILD-TYPE 
         14.730          14.155 
[1] "0.0 - 75.1 (14.7)" "0.2 - 71.7 (14.2)"
[1] "hr=" "1.1"
D4V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RIOK1 MUTATED          1        4         8        40         1        1
  RIOK1 WILD-TYPE        2        4        15        63         3        3
D4V3, multiclass
           clus
vv          RIOK1 MUTATED RIOK1 WILD-TYPE
  STAGE IA              1               2
  STAGE IB              4               4
  STAGE IIA             8              15
  STAGE IIB            40              63
  STAGE III             1               3
  STAGE IV              1               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
  RIOK1 MUTATED    2  8    45
  RIOK1 WILD-TYPE  2  8    80
D4V4, multiclass
       clus
vv      RIOK1 MUTATED RIOK1 WILD-TYPE
  T1                2               2
  T2                8               8
  T3+T4            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"
D4V5, binary
                 cls
clus               0  1
  RIOK1 MUTATED   12 43
  RIOK1 WILD-TYPE 25 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED     12   43
  RIOK1 WILD-TYPE   25   65
   clus
vv  RIOK1 MUTATED RIOK1 WILD-TYPE
  0            12              25
  1            43              65
[1] 2 2
[1] FALSE
D4V6, binary
                 cls
clus               0  1
  RIOK1 MUTATED   28  1
  RIOK1 WILD-TYPE 38  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED     28    1
  RIOK1 WILD-TYPE   38    3
   clus
vv  RIOK1 MUTATED RIOK1 WILD-TYPE
  0            28              38
  1             1               3
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus               0  1
  RIOK1 MUTATED   32 23
  RIOK1 WILD-TYPE 35 56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED     32   23
  RIOK1 WILD-TYPE   35   56
        clus
vv       RIOK1 MUTATED RIOK1 WILD-TYPE
  FEMALE            32              35
  MALE              23              56
[1] 2 2
[1] FALSE
D4V8, binary
                 cls
clus               0  1
  RIOK1 MUTATED   38 10
  RIOK1 WILD-TYPE 56 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED     38   10
  RIOK1 WILD-TYPE   56   26
     clus
vv    RIOK1 MUTATED RIOK1 WILD-TYPE
  NO             38              56
  YES            10              26
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RIOK1 MUTATED                                    49
  RIOK1 WILD-TYPE                                  81
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RIOK1 MUTATED                                       4
  RIOK1 WILD-TYPE                                     9
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RIOK1 MUTATED                                                  2
  RIOK1 WILD-TYPE                                                0
D4V9, multiclass
                                                  clus
vv                                                 RIOK1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         49
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             2
                                                  clus
vv                                                 RIOK1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           81
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          9
  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"
D4V10, continuous
D4V11, continuous
                 vv
clus              R0 R1 R2 RX
  RIOK1 MUTATED   28 19  1  1
  RIOK1 WILD-TYPE 51 31  3  2
D4V12, multiclass
    clus
vv   RIOK1 MUTATED RIOK1 WILD-TYPE
  R0            28              51
  R1            19              31
  R2             1               3
  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"
D4V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RIOK1 MUTATED       5                         1    46
  RIOK1 WILD-TYPE     4                         4    82
D4V14, multiclass
                           clus
vv                          RIOK1 MUTATED RIOK1 WILD-TYPE
  ASIAN                                 5               4
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                46              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                 cls
clus               0  1
  RIOK1 MUTATED    2 38
  RIOK1 WILD-TYPE  3 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIOK1 MUTATED      2   38
  RIOK1 WILD-TYPE    3   67
                        clus
vv                       RIOK1 MUTATED RIOK1 WILD-TYPE
  HISPANIC OR LATINO                 2               3
  NOT HISPANIC OR LATINO            38              67
[1] 2 2
[1] FALSE

Clustering(5) Variable = LCE2A MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2              0  1
  LCE2A MUTATED   20 26
  LCE2A WILD-TYPE 48 50
  LCE2A MUTATED LCE2A WILD-TYPE 
             46              98 
  LCE2A MUTATED LCE2A WILD-TYPE 
             26              50 
$`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 
        0.03         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ3 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8315 
        1.02         8.28        30.25        20.19        17.03         9.83 
TCGA-HZ-8317 TCGA-HZ-A49H TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7886 TCGA-IB-7887 
       12.43        16.14        19.82        12.95         4.04         3.62 
TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-A6UG TCGA-IB-AAUP TCGA-IB-AAUU TCGA-LB-A7SX 
       15.81         3.85         1.35        14.17         8.05        12.92 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RP TCGA-US-A776 
       12.46        19.20        15.32         9.40        23.08        39.98 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-YB-A89D TCGA-YY-A8LH 
       13.81        12.99        11.51        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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IZ 
       43.50         7.36        24.26        33.57        15.06        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H TCGA-F2-A7TX 
       24.43        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        12.66        16.37         4.04         5.03 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
       17.49        19.50         0.13        23.21        12.03        19.59 
TCGA-HZ-8005 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49I TCGA-HZ-A4BH 
        3.95        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-7645 
       21.60         5.26        10.85         1.08         0.23        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-7888 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       43.79        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-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN TCGA-IB-AAUO TCGA-IB-AAUQ 
        8.22        15.88         0.26         4.73         7.86         6.02 
TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-LB-A9Q5 TCGA-OE-A75W TCGA-PZ-A5RE 
       11.11         7.40         9.44        10.29         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A779 
       13.68         3.12        24.23        17.26        22.85        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       14.14         0.39        12.03        16.37        31.27        23.67 
TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.76        15.35 

  LCE2A MUTATED LCE2A WILD-TYPE 
           0.03            0.13 
  LCE2A MUTATED LCE2A WILD-TYPE 
          66.28           75.12 
  LCE2A MUTATED LCE2A WILD-TYPE 
          12.97           15.09 
[1] "0.0 - 66.3 (13.0)" "0.1 - 75.1 (15.1)"
[1] "hr=" "1.3"
D5V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  LCE2A MUTATED          1        0        10        31         1        3
  LCE2A WILD-TYPE        2        8        13        72         3        1
D5V3, multiclass
           clus
vv          LCE2A MUTATED LCE2A WILD-TYPE
  STAGE IA              1               2
  STAGE IB              0               8
  STAGE IIA            10              13
  STAGE IIB            31              72
  STAGE III             1               3
  STAGE IV              3               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    41
  LCE2A WILD-TYPE  2 13    84
D5V4, multiclass
       clus
vv      LCE2A MUTATED LCE2A WILD-TYPE
  T1                2               2
  T2                3              13
  T3+T4            41              84
[1] 3 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   13 33
  LCE2A WILD-TYPE 24 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2A MUTATED     13   33
  LCE2A WILD-TYPE   24   75
   clus
vv  LCE2A MUTATED LCE2A WILD-TYPE
  0            13              24
  1            33              75
[1] 2 2
[1] FALSE
D5V6, binary
                 cls
clus               0  1
  LCE2A MUTATED   17  3
  LCE2A WILD-TYPE 49  1
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2A MUTATED     17    3
  LCE2A WILD-TYPE   49    1
   clus
vv  LCE2A MUTATED LCE2A WILD-TYPE
  0            17              49
  1             3               1
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus               0  1
  LCE2A MUTATED   20 26
  LCE2A WILD-TYPE 47 53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2A MUTATED     20   26
  LCE2A WILD-TYPE   47   53
        clus
vv       LCE2A MUTATED LCE2A WILD-TYPE
  FEMALE            20              47
  MALE              26              53
[1] 2 2
[1] FALSE
D5V8, binary
                 cls
clus               0  1
  LCE2A MUTATED   28 15
  LCE2A WILD-TYPE 66 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2A MUTATED     28   15
  LCE2A WILD-TYPE   66   21
     clus
vv    LCE2A MUTATED LCE2A WILD-TYPE
  NO             28              66
  YES            15              21
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LCE2A MUTATED                                    41
  LCE2A WILD-TYPE                                  89
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LCE2A MUTATED                                       4
  LCE2A WILD-TYPE                                     9
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LCE2A MUTATED                                                  1
  LCE2A WILD-TYPE                                                1
D5V9, multiclass
                                                  clus
vv                                                 LCE2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         41
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 LCE2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           89
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          9
  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"
D5V10, continuous
D5V11, continuous
                 vv
clus              R0 R1 R2 RX
  LCE2A MUTATED   27 14  3  1
  LCE2A WILD-TYPE 52 36  1  2
D5V12, multiclass
    clus
vv   LCE2A MUTATED LCE2A WILD-TYPE
  R0            27              52
  R1            14              36
  R2             3               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"
D5V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LCE2A MUTATED       3                         3    39
  LCE2A WILD-TYPE     6                         2    89
D5V14, multiclass
                           clus
vv                          LCE2A MUTATED LCE2A WILD-TYPE
  ASIAN                                 3               6
  BLACK OR AFRICAN AMERICAN             3               2
  WHITE                                39              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"
D5V15, binary
                 cls
clus               0  1
  LCE2A MUTATED    0 33
  LCE2A WILD-TYPE  5 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LCE2A MUTATED      0   33
  LCE2A WILD-TYPE    5   72
                        clus
vv                       LCE2A MUTATED LCE2A WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            33              72
[1] 2 2
[1] FALSE

Clustering(6) Variable = C1QB MUTATION ANALYSIS
D6V1, survival
                sevent
clus2             0  1
  C1QB MUTATED   12 23
  C1QB WILD-TYPE 56 53
  C1QB MUTATED C1QB WILD-TYPE 
            35            109 
  C1QB MUTATED C1QB WILD-TYPE 
            23             53 
$`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        42.31        15.91         9.11 
TCGA-2J-AABV TCGA-3A-A9I5 TCGA-3A-A9IB TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-FB-A4P6 
       21.44        58.98         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-HV-A5A4 TCGA-HV-A5A6 TCGA-HZ-7926 TCGA-HZ-A77P TCGA-IB-7644 
       13.84         7.63        66.94        17.03        10.85        12.95 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7888 TCGA-IB-A6UG 
        4.77        21.90        19.82        23.80        43.79         1.35 
TCGA-IB-AAUQ TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A779 TCGA-Z5-AAPL 
        6.02         8.78        13.68        16.80        15.35 

$`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 
       43.50        20.84        24.26        33.57        15.06        24.43 
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        12.66        16.37         0.03         7.50 
TCGA-FB-AAQ0 TCGA-H6-8124 TCGA-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HV-AA8V 
       15.55        12.89         4.21         9.50         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 
       17.49        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 
       19.59         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-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7649 TCGA-IB-7885 
        1.08         0.23        19.82        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        39.98        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  C1QB MUTATED C1QB WILD-TYPE 
          1.02           0.03 
  C1QB MUTATED C1QB WILD-TYPE 
         66.94          75.12 
  C1QB MUTATED C1QB WILD-TYPE 
         13.68          14.47 
[1] "1.0 - 66.9 (13.7)" "0.0 - 75.1 (14.5)"
[1] "hr=" "1.3"
D6V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  C1QB MUTATED          1        0         7        25         0        1
  C1QB WILD-TYPE        2        8        16        78         4        3
D6V3, multiclass
           clus
vv          C1QB MUTATED C1QB WILD-TYPE
  STAGE IA             1              2
  STAGE IB             0              8
  STAGE IIA            7             16
  STAGE IIB           25             78
  STAGE III            0              4
  STAGE IV             1              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
  C1QB MUTATED    1  2    31
  C1QB WILD-TYPE  3 14    94
D6V4, multiclass
       clus
vv      C1QB MUTATED C1QB WILD-TYPE
  T1               1              3
  T2               2             14
  T3+T4           31             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"
D6V5, binary
                cls
clus              0  1
  C1QB MUTATED    9 26
  C1QB WILD-TYPE 28 82
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QB MUTATED      9   26
  C1QB WILD-TYPE   28   82
   clus
vv  C1QB MUTATED C1QB WILD-TYPE
  0            9             28
  1           26             82
[1] 2 2
[1] FALSE
D6V6, binary
                cls
clus              0  1
  C1QB MUTATED   17  1
  C1QB WILD-TYPE 49  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QB MUTATED     17    1
  C1QB WILD-TYPE   49    3
   clus
vv  C1QB MUTATED C1QB WILD-TYPE
  0           17             49
  1            1              3
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus              0  1
  C1QB MUTATED   14 21
  C1QB WILD-TYPE 53 58
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QB MUTATED     14   21
  C1QB WILD-TYPE   53   58
        clus
vv       C1QB MUTATED C1QB WILD-TYPE
  FEMALE           14             53
  MALE             21             58
[1] 2 2
[1] FALSE
D6V8, binary
                cls
clus              0  1
  C1QB MUTATED   25  7
  C1QB WILD-TYPE 69 29
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QB MUTATED     25    7
  C1QB WILD-TYPE   69   29
     clus
vv    C1QB MUTATED C1QB WILD-TYPE
  NO            25             69
  YES            7             29
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C1QB MUTATED                                    32
  C1QB WILD-TYPE                                  98
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C1QB MUTATED                                       3
  C1QB WILD-TYPE                                    10
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C1QB MUTATED                                                  0
  C1QB WILD-TYPE                                                2
D6V9, multiclass
                                                  clus
vv                                                 C1QB MUTATED C1QB WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        32             98
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3             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"
D6V10, continuous
D6V11, continuous
                vv
clus             R0 R1 R2 RX
  C1QB MUTATED   18 13  0  1
  C1QB WILD-TYPE 61 37  4  2
D6V12, multiclass
    clus
vv   C1QB MUTATED C1QB WILD-TYPE
  R0           18             61
  R1           13             37
  R2            0              4
  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"
D6V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1QB MUTATED       4                         2    29
  C1QB WILD-TYPE     5                         3    99
D6V14, multiclass
                           clus
vv                          C1QB MUTATED C1QB WILD-TYPE
  ASIAN                                4              5
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                               29             99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                cls
clus              0  1
  C1QB MUTATED    1 25
  C1QB WILD-TYPE  4 80
[1] "tbl2"
                cls
clus             [,1] [,2]
  C1QB MUTATED      1   25
  C1QB WILD-TYPE    4   80
                        clus
vv                       C1QB MUTATED C1QB WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO           25             80
[1] 2 2
[1] FALSE

Clustering(7) Variable = SMAD4 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2              0  1
  SMAD4 MUTATED   14 17
  SMAD4 WILD-TYPE 54 59
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             31             113 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             17              59 
$`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        33.57        34.09        71.74 
TCGA-FB-A78T TCGA-FB-AAPY TCGA-FB-AAQ3 TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-AA8V 
        0.03        34.82         1.02         4.21         7.63        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-A77Q TCGA-IB-7644 
       17.49        19.50         9.83        12.43         1.08        12.95 
TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-A5SP TCGA-IB-AAUM 
       19.82         4.04        15.81        21.30        15.85         0.26 
TCGA-IB-AAUR TCGA-LB-A9Q5 TCGA-PZ-A5RE TCGA-S4-A8RM TCGA-S4-A8RP TCGA-US-A77G 
       11.11        10.29        15.45        24.23        23.08         0.39 
TCGA-YB-A89D 
       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        42.31 
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        58.98        43.50 
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        24.43 
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        12.66        16.37         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-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
        9.50        66.94         8.28         0.13        20.19        17.03 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8519 TCGA-HZ-8636 
       23.21        12.03        19.59         3.95        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-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
       10.85         0.23        19.82        49.38         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7890 
       15.35        23.80        41.33         3.62        43.79        19.66 
TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ 
        3.85        15.98         2.47        17.16        12.00         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-AAUQ TCGA-IB-AAUS TCGA-IB-AAUT 
        4.73         7.86        14.17         6.02         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY 
        8.05        12.92        12.46        19.20         8.78        13.68 
TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A776 
        3.12        15.32         9.40        17.26        22.85        39.98 
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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.03            0.13 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          71.74           75.12 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          15.45           14.17 
[1] "0.0 - 71.7 (15.4)" "0.1 - 75.1 (14.2)"
[1] "hr=" "1"  
D7V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SMAD4 MUTATED          2        0         6        23         0        1
  SMAD4 WILD-TYPE        1        8        17        80         4        3
D7V3, multiclass
           clus
vv          SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE IA              2               1
  STAGE IB              0               8
  STAGE IIA             6              17
  STAGE IIB            23              80
  STAGE III             0               4
  STAGE IV              1               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
  SMAD4 MUTATED    2  3    27
  SMAD4 WILD-TYPE  2 13    98
D7V4, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T1                2               2
  T2                3              13
  T3+T4            27              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"
D7V5, binary
                 cls
clus               0  1
  SMAD4 MUTATED    7 24
  SMAD4 WILD-TYPE 30 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      7   24
  SMAD4 WILD-TYPE   30   84
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0             7              30
  1            24              84
[1] 2 2
[1] FALSE
D7V6, binary
                 cls
clus               0  1
  SMAD4 MUTATED   12  1
  SMAD4 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     12    1
  SMAD4 WILD-TYPE   54    3
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0            12              54
  1             1               3
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus               0  1
  SMAD4 MUTATED   16 16
  SMAD4 WILD-TYPE 51 63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     16   16
  SMAD4 WILD-TYPE   51   63
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE            16              51
  MALE              16              63
[1] 2 2
[1] FALSE
D7V8, binary
                 cls
clus               0  1
  SMAD4 MUTATED   17  8
  SMAD4 WILD-TYPE 77 28
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     17    8
  SMAD4 WILD-TYPE   77   28
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO             17              77
  YES             8              28
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMAD4 MUTATED                                    31
  SMAD4 WILD-TYPE                                  99
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMAD4 MUTATED                                       1
  SMAD4 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMAD4 MUTATED                                                  0
  SMAD4 WILD-TYPE                                                2
D7V9, multiclass
                                                  clus
vv                                                 SMAD4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         31
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SMAD4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           99
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D7V10, continuous
D7V11, continuous
                 vv
clus              R0 R1 R2 RX
  SMAD4 MUTATED   17  9  2  0
  SMAD4 WILD-TYPE 62 41  2  3
D7V12, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            17              62
  R1             9              41
  R2             2               2
  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"
D7V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED       4                         0    28
  SMAD4 WILD-TYPE     5                         5   100
D7V14, multiclass
                           clus
vv                          SMAD4 MUTATED SMAD4 WILD-TYPE
  ASIAN                                 4               5
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                28             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"
D7V15, binary
                 cls
clus               0  1
  SMAD4 MUTATED    1 22
  SMAD4 WILD-TYPE  4 83
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1   22
  SMAD4 WILD-TYPE    4   83
                        clus
vv                       SMAD4 MUTATED SMAD4 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO            22              83
[1] 2 2
[1] FALSE

Clustering(8) Variable = CDKN2A MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED   12 17
  CDKN2A WILD-TYPE 56 59
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              29              115 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              17               59 
$`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        43.50 
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        12.66         0.03 
TCGA-H6-8124 TCGA-HV-A7OL TCGA-HZ-7926 TCGA-HZ-8005 TCGA-HZ-A49G TCGA-HZ-A4BH 
       12.89         8.28        17.03         3.95        21.70         6.38 
TCGA-HZ-A77O TCGA-HZ-A9TJ TCGA-IB-7649 TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-8127 
        5.26        19.82        15.35         4.04        15.81        17.16 
TCGA-IB-A5SS TCGA-IB-A6UG TCGA-OE-A75W TCGA-RB-AA9M TCGA-US-A77G 
       15.12         1.35         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 
       42.31        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        58.98        20.84        24.26        33.57 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ TCGA-F2-A44G TCGA-F2-A44H 
       34.09        10.13        24.43        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        16.37         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
        1.02        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 
       30.25        17.49        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        19.59         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80        14.14        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.03             0.13 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           75.12            71.74 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           12.95            14.40 
[1] "0.0 - 75.1 (12.9)" "0.1 - 71.7 (14.4)"
[1] "hr=" "1.3"
D8V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CDKN2A MUTATED          0        0         2        26         1        1
  CDKN2A WILD-TYPE        3        8        21        77         3        3
D8V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              2               21
  STAGE IIB             26               77
  STAGE III              1                3
  STAGE IV               1                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    27
  CDKN2A WILD-TYPE  3 14    98
D8V4, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T1                 1                3
  T2                 2               14
  T3+T4             27               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"
D8V5, binary
                  cls
clus                0  1
  CDKN2A MUTATED    4 26
  CDKN2A WILD-TYPE 33 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      4   26
  CDKN2A WILD-TYPE   33   82
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0              4               33
  1             26               82
[1] 2 2
[1] FALSE
D8V6, binary
                  cls
clus                0  1
  CDKN2A MUTATED   15  1
  CDKN2A WILD-TYPE 51  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     15    1
  CDKN2A WILD-TYPE   51    3
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             15               51
  1              1                3
[1] 2 2
[1] FALSE
D8V7, binary
                  cls
clus                0  1
  CDKN2A MUTATED   11 19
  CDKN2A WILD-TYPE 56 60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     11   19
  CDKN2A WILD-TYPE   56   60
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE             11               56
  MALE               19               60
[1] 2 2
[1] FALSE
D8V8, binary
                  cls
clus                0  1
  CDKN2A MUTATED   17  9
  CDKN2A WILD-TYPE 77 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     17    9
  CDKN2A WILD-TYPE   77   27
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              17               77
  YES              9               27
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDKN2A MUTATED                                    28
  CDKN2A WILD-TYPE                                 102
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDKN2A MUTATED                                       2
  CDKN2A WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDKN2A MUTATED                                                  0
  CDKN2A WILD-TYPE                                                2
D8V9, multiclass
                                                  clus
vv                                                 CDKN2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          28
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 CDKN2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           102
  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"
D8V10, continuous
D8V11, continuous
                  vv
clus               R0 R1 R2 RX
  CDKN2A MUTATED   16 10  1  1
  CDKN2A WILD-TYPE 63 40  3  2
D8V12, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0             16               63
  R1             10               40
  R2              1                3
  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"
D8V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       1                         2    26
  CDKN2A WILD-TYPE     8                         3   102
D8V14, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  1                8
  BLACK OR AFRICAN AMERICAN              2                3
  WHITE                                 26              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"
D8V15, binary
                  cls
clus                0  1
  CDKN2A MUTATED    0 21
  CDKN2A WILD-TYPE  5 84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      0   21
  CDKN2A WILD-TYPE    5   84
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             21               84
[1] 2 2
[1] FALSE

Clustering(9) Variable = MLL2 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2             0  1
  MLL2 MUTATED   13 16
  MLL2 WILD-TYPE 55 60
  MLL2 MUTATED MLL2 WILD-TYPE 
            29            115 
  MLL2 MUTATED MLL2 WILD-TYPE 
            16             60 
$`MLL2 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AAB6 TCGA-2J-AAB8 TCGA-2J-AABU TCGA-2L-AAQE TCGA-3A-A9I9 
       23.97         9.63         2.63         9.11        22.49        20.84 
TCGA-3A-A9IU TCGA-3A-A9J0 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A78T TCGA-FB-AAPU 
       15.06        24.43         7.66        19.27         0.03        12.53 
TCGA-FB-AAQ0 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-IB-7645 
       15.55        20.19        17.03        21.70         6.38        49.38 
TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-Q3-A5QY 
       19.82         4.04        17.16        15.85        15.12        13.68 
TCGA-RB-A7B8 TCGA-US-A774 TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YY-A8LH 
       15.32        22.85        16.37        23.67        66.28 

$`MLL2 WILD-TYPE`
TCGA-2J-AAB1 TCGA-2J-AAB9 TCGA-2J-AABA TCGA-2J-AABE TCGA-2J-AABF TCGA-2J-AABH 
        2.17        20.61        19.96        22.22        22.72        42.31 
TCGA-2J-AABK TCGA-2J-AABO TCGA-2J-AABR TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI 
       15.91        14.47        14.40        21.44         4.70         3.39 
TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-3A-A9IC 
       12.95         9.60        58.98        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       33.57        34.09        10.13        75.12        71.74        10.98 
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        12.66        16.37 
TCGA-FB-AAPS TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 
        7.50        34.82        23.54         4.04         5.03         1.02 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 
        8.28        30.25        17.49        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        19.59         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
       17.92        16.14        10.13        21.60         5.26        10.85 
TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7647 
        1.08         0.23        19.82        12.95         4.77        21.90 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       15.35        23.80        41.33         3.62        43.79        15.81 
TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
       19.66        21.30         3.85        15.98         2.47        12.00 
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-AA2A TCGA-RB-AA9M TCGA-S4-A8RM 
       19.20         8.78        15.45         3.12         9.40        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       17.26        23.08        39.98        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY 
       13.81        12.99        12.03        31.27        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.03           0.13 
  MLL2 MUTATED MLL2 WILD-TYPE 
         66.28          75.12 
  MLL2 MUTATED MLL2 WILD-TYPE 
         16.37          12.95 
[1] "0.0 - 66.3 (16.4)" "0.1 - 75.1 (12.9)"
[1] "hr=" "1.1"
D9V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MLL2 MUTATED          0        1         7        21         0        0
  MLL2 WILD-TYPE        3        7        16        82         4        4
D9V3, multiclass
           clus
vv          MLL2 MUTATED MLL2 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             1              7
  STAGE IIA            7             16
  STAGE IIB           21             82
  STAGE III            0              4
  STAGE IV             0              4
[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
  MLL2 MUTATED    0  3    26
  MLL2 WILD-TYPE  4 13    99
D9V4, multiclass
       clus
vv      MLL2 MUTATED MLL2 WILD-TYPE
  T1               0              4
  T2               3             13
  T3+T4           26             99
[1] 3 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
  MLL2 MUTATED    8 21
  MLL2 WILD-TYPE 29 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      8   21
  MLL2 WILD-TYPE   29   87
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0            8             29
  1           21             87
[1] 2 2
[1] FALSE
D9V6, binary
                cls
clus              0  1
  MLL2 MUTATED   15  0
  MLL2 WILD-TYPE 51  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     15    0
  MLL2 WILD-TYPE   51    4
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           15             51
  1            0              4
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus              0  1
  MLL2 MUTATED   11 18
  MLL2 WILD-TYPE 56 61
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     11   18
  MLL2 WILD-TYPE   56   61
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           11             56
  MALE             18             61
[1] 2 2
[1] FALSE
D9V8, binary
                cls
clus              0  1
  MLL2 MUTATED   19  6
  MLL2 WILD-TYPE 75 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     19    6
  MLL2 WILD-TYPE   75   30
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            19             75
  YES            6             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MLL2 MUTATED                                    26
  MLL2 WILD-TYPE                                 104
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MLL2 MUTATED                                       3
  MLL2 WILD-TYPE                                    10
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MLL2 MUTATED                                                  0
  MLL2 WILD-TYPE                                                2
D9V9, multiclass
                                                  clus
vv                                                 MLL2 MUTATED MLL2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        26            104
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       3             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"
D9V10, continuous
D9V11, continuous
                vv
clus             R0 R1 R2 RX
  MLL2 MUTATED   19  9  0  1
  MLL2 WILD-TYPE 60 41  4  2
D9V12, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           19             60
  R1            9             41
  R2            0              4
  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"
D9V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED       1                         1    26
  MLL2 WILD-TYPE     8                         4   102
D9V14, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                1              8
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                               26            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"
D9V15, binary
                cls
clus              0  1
  MLL2 MUTATED    1 20
  MLL2 WILD-TYPE  4 85
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      1   20
  MLL2 WILD-TYPE    4   85
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO           20             85
[1] 2 2
[1] FALSE

Clustering(10) Variable = AEBP1 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  AEBP1 MUTATED   13 13
  AEBP1 WILD-TYPE 55 63
  AEBP1 MUTATED AEBP1 WILD-TYPE 
             26             118 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
             13              63 
$`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        39.98         0.39 
TCGA-XN-A8T3 TCGA-YY-A8LH 
       31.27        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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX 
       43.50        20.84        24.26        33.57        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        24.43        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        12.66        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        5.03         1.02        12.89         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7925 
       66.94         8.28        30.25        17.49        19.50        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        19.59         3.95         9.83 
TCGA-HZ-8636 TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q 
       17.92        16.14        10.13        21.60         5.26         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        0.23        19.82        15.35        23.80        41.33         4.04 
TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
        3.62        43.79        15.81         3.85        15.98         2.47 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       17.16        12.00         7.20        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        24.23        17.26        23.08        22.85 
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        16.37 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       23.67        11.51        12.76        15.35 

  AEBP1 MUTATED AEBP1 WILD-TYPE 
           0.13            0.03 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
          66.28           75.12 
  AEBP1 MUTATED AEBP1 WILD-TYPE 
         15.485          13.975 
[1] "0.1 - 66.3 (15.5)" "0.0 - 75.1 (14.0)"
[1] "hr=" "1.2"
D10V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AEBP1 MUTATED          1        2         4        18         0        1
  AEBP1 WILD-TYPE        2        6        19        85         4        3
D10V3, multiclass
           clus
vv          AEBP1 MUTATED AEBP1 WILD-TYPE
  STAGE IA              1               2
  STAGE IB              2               6
  STAGE IIA             4              19
  STAGE IIB            18              85
  STAGE III             0               4
  STAGE IV              1               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
  AEBP1 MUTATED     1   3    22
  AEBP1 WILD-TYPE   3  13   103
D10V4, multiclass
       clus
vv      AEBP1 MUTATED AEBP1 WILD-TYPE
  T1                1               3
  T2                3              13
  T3+T4            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"
D10V5, binary
                 cls
clus               0  1
  AEBP1 MUTATED    7 19
  AEBP1 WILD-TYPE 30 89
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED      7   19
  AEBP1 WILD-TYPE   30   89
   clus
vv  AEBP1 MUTATED AEBP1 WILD-TYPE
  0             7              30
  1            19              89
[1] 2 2
[1] FALSE
D10V6, binary
                 cls
clus               0  1
  AEBP1 MUTATED   12  1
  AEBP1 WILD-TYPE 54  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED     12    1
  AEBP1 WILD-TYPE   54    3
   clus
vv  AEBP1 MUTATED AEBP1 WILD-TYPE
  0            12              54
  1             1               3
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus               0  1
  AEBP1 MUTATED   13 13
  AEBP1 WILD-TYPE 54 66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED     13   13
  AEBP1 WILD-TYPE   54   66
        clus
vv       AEBP1 MUTATED AEBP1 WILD-TYPE
  FEMALE            13              54
  MALE              13              66
[1] 2 2
[1] FALSE
D10V8, binary
                 cls
clus               0  1
  AEBP1 MUTATED   16  7
  AEBP1 WILD-TYPE 78 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED     16    7
  AEBP1 WILD-TYPE   78   29
     clus
vv    AEBP1 MUTATED AEBP1 WILD-TYPE
  NO             16              78
  YES             7              29
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AEBP1 MUTATED                                    22
  AEBP1 WILD-TYPE                                 108
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AEBP1 MUTATED                                       3
  AEBP1 WILD-TYPE                                    10
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AEBP1 MUTATED                                                  1
  AEBP1 WILD-TYPE                                                1
D10V9, multiclass
                                                  clus
vv                                                 AEBP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 AEBP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          108
  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"
D10V10, continuous
D10V11, continuous
                 vv
clus              R0 R1 R2 RX
  AEBP1 MUTATED   16  9  0  0
  AEBP1 WILD-TYPE 63 41  4  3
D10V12, multiclass
    clus
vv   AEBP1 MUTATED AEBP1 WILD-TYPE
  R0            16              63
  R1             9              41
  R2             0               4
  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"
D10V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AEBP1 MUTATED       0                         0    24
  AEBP1 WILD-TYPE     9                         5   104
D10V14, multiclass
                           clus
vv                          AEBP1 MUTATED AEBP1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                24             104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                 cls
clus               0  1
  AEBP1 MUTATED    1 19
  AEBP1 WILD-TYPE  4 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AEBP1 MUTATED      1   19
  AEBP1 WILD-TYPE    4   86
                        clus
vv                       AEBP1 MUTATED AEBP1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO            19              86
[1] 2 2
[1] FALSE

Clustering(11) Variable = RBM47 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2              0  1
  RBM47 MUTATED    9 14
  RBM47 WILD-TYPE 59 62
  RBM47 MUTATED RBM47 WILD-TYPE 
             23             121 
  RBM47 MUTATED RBM47 WILD-TYPE 
             14              62 
$`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        42.31        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ 
       20.84         7.36        24.26        33.57        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       24.43        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        12.66        16.37         0.03 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HV-A5A3 
       23.54         4.04         1.02        12.89        13.84         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
        7.63         9.50        66.94         8.28        30.25        17.49 
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        19.59 
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-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       10.13         6.38        21.60         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       19.82        49.38         4.77        21.90        15.35        23.80 
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-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-AAUR TCGA-IB-AAUS TCGA-IB-AAUT 
        4.73         7.86        14.17        11.11         7.40         9.44 
TCGA-IB-AAUU TCGA-LB-A8F3 TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        8.05        12.46        10.29        19.20         8.78        15.45 
TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       13.68         3.12        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  RBM47 MUTATED RBM47 WILD-TYPE 
           1.08            0.03 
  RBM47 MUTATED RBM47 WILD-TYPE 
          66.28           75.12 
  RBM47 MUTATED RBM47 WILD-TYPE 
          15.06           14.14 
[1] "1.1 - 66.3 (15.1)" "0.0 - 75.1 (14.1)"
[1] "hr=" "1.1"
D11V2, 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        3        8        19        83         4        3
D11V3, multiclass
           clus
vv          RBM47 MUTATED RBM47 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             4              19
  STAGE IIB            20              83
  STAGE III             0               4
  STAGE IV              1               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
  RBM47 MUTATED     1   2    22
  RBM47 WILD-TYPE   3  14   103
D11V4, multiclass
       clus
vv      RBM47 MUTATED RBM47 WILD-TYPE
  T1                1               3
  T2                2              14
  T3+T4            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"
D11V5, binary
                 cls
clus               0  1
  RBM47 MUTATED    4 21
  RBM47 WILD-TYPE 33 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM47 MUTATED      4   21
  RBM47 WILD-TYPE   33   87
   clus
vv  RBM47 MUTATED RBM47 WILD-TYPE
  0             4              33
  1            21              87
[1] 2 2
[1] FALSE
D11V6, binary
                 cls
clus               0  1
  RBM47 MUTATED    8  1
  RBM47 WILD-TYPE 58  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM47 MUTATED      8    1
  RBM47 WILD-TYPE   58    3
   clus
vv  RBM47 MUTATED RBM47 WILD-TYPE
  0             8              58
  1             1               3
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus               0  1
  RBM47 MUTATED   16  9
  RBM47 WILD-TYPE 51 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM47 MUTATED     16    9
  RBM47 WILD-TYPE   51   70
        clus
vv       RBM47 MUTATED RBM47 WILD-TYPE
  FEMALE            16              51
  MALE               9              70
[1] 2 2
[1] FALSE
D11V8, binary
                 cls
clus               0  1
  RBM47 MUTATED   15  6
  RBM47 WILD-TYPE 79 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM47 MUTATED     15    6
  RBM47 WILD-TYPE   79   30
     clus
vv    RBM47 MUTATED RBM47 WILD-TYPE
  NO             15              79
  YES             6              30
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM47 MUTATED                                    23
  RBM47 WILD-TYPE                                 107
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM47 MUTATED                                       2
  RBM47 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM47 MUTATED                                                  0
  RBM47 WILD-TYPE                                                2
D11V9, 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                          107
  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"
D11V10, continuous
D11V11, continuous
                 vv
clus              R0 R1 R2 RX
  RBM47 MUTATED   16  8  0  0
  RBM47 WILD-TYPE 63 42  4  3
D11V12, multiclass
    clus
vv   RBM47 MUTATED RBM47 WILD-TYPE
  R0            16              63
  R1             8              42
  R2             0               4
  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"
D11V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM47 MUTATED       1                         2    22
  RBM47 WILD-TYPE     8                         3   106
D11V14, multiclass
                           clus
vv                          RBM47 MUTATED RBM47 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                22             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"
D11V15, binary
                 cls
clus               0  1
  RBM47 MUTATED    1 21
  RBM47 WILD-TYPE  4 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM47 MUTATED      1   21
  RBM47 WILD-TYPE    4   84
                        clus
vv                       RBM47 MUTATED RBM47 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO            21              84
[1] 2 2
[1] FALSE

Clustering(12) Variable = ANKRD36 MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  ANKRD36 MUTATED   11 13
  ANKRD36 WILD-TYPE 57 63
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               24               120 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
               13                63 
$`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        19.59        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        24.23 
TCGA-S4-A8RP TCGA-US-A77E TCGA-XD-AAUG TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       23.08        14.14        13.81        23.67        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 
       42.31        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        58.98        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
        7.36        24.26        33.57        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       24.43        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        12.66        16.37         0.03 
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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        5.03        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-A49G TCGA-HZ-A49H 
       17.03        12.03         3.95         9.83        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       17.16        12.00        15.85        15.12        20.88        21.90 
TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUO TCGA-IB-AAUP 
        1.35         8.22        15.88         0.26         7.86        14.17 
TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS TCGA-IB-AAUT TCGA-LB-A7SX TCGA-LB-A8F3 
        6.02        11.11         7.40         9.44        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-A8RO TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
        9.40        17.26        22.85        39.98        16.80         0.39 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-YH-A8SY TCGA-Z5-AAPL 
       12.99        12.03        16.37        31.27        12.76        15.35 

  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
             1.02              0.03 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
            66.28             75.12 
  ANKRD36 MUTATED ANKRD36 WILD-TYPE 
           15.965            14.005 
[1] "1.0 - 66.3 (16.0)" "0.0 - 75.1 (14.0)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ANKRD36 MUTATED          1        3         2        14         2        2
  ANKRD36 WILD-TYPE        2        5        21        89         2        2
D12V3, multiclass
           clus
vv          ANKRD36 MUTATED ANKRD36 WILD-TYPE
  STAGE IA                1                 2
  STAGE IB                3                 5
  STAGE IIA               2                21
  STAGE IIB              14                89
  STAGE III               2                 2
  STAGE IV                2                 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
  ANKRD36 MUTATED     1   3    20
  ANKRD36 WILD-TYPE   3  13   105
D12V4, multiclass
       clus
vv      ANKRD36 MUTATED ANKRD36 WILD-TYPE
  T1                  1                 3
  T2                  3                13
  T3+T4              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"
D12V5, binary
                   cls
clus                 0  1
  ANKRD36 MUTATED    8 16
  ANKRD36 WILD-TYPE 29 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED      8   16
  ANKRD36 WILD-TYPE   29   92
   clus
vv  ANKRD36 MUTATED ANKRD36 WILD-TYPE
  0               8                29
  1              16                92
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  ANKRD36 MUTATED    9  2
  ANKRD36 WILD-TYPE 57  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED      9    2
  ANKRD36 WILD-TYPE   57    2
   clus
vv  ANKRD36 MUTATED ANKRD36 WILD-TYPE
  0               9                57
  1               2                 2
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  ANKRD36 MUTATED   12 12
  ANKRD36 WILD-TYPE 55 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED     12   12
  ANKRD36 WILD-TYPE   55   67
        clus
vv       ANKRD36 MUTATED ANKRD36 WILD-TYPE
  FEMALE              12                55
  MALE                12                67
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                 0  1
  ANKRD36 MUTATED   13  9
  ANKRD36 WILD-TYPE 81 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED     13    9
  ANKRD36 WILD-TYPE   81   27
     clus
vv    ANKRD36 MUTATED ANKRD36 WILD-TYPE
  NO               13                81
  YES               9                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANKRD36 MUTATED                                    21
  ANKRD36 WILD-TYPE                                 109
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANKRD36 MUTATED                                       3
  ANKRD36 WILD-TYPE                                    10
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANKRD36 MUTATED                                                  0
  ANKRD36 WILD-TYPE                                                2
D12V9, multiclass
                                                  clus
vv                                                 ANKRD36 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 ANKRD36 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            109
  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"
D12V10, continuous
D12V11, continuous
                   vv
clus                R0 R1 R2 RX
  ANKRD36 MUTATED   14  9  0  1
  ANKRD36 WILD-TYPE 65 41  4  2
D12V12, multiclass
    clus
vv   ANKRD36 MUTATED ANKRD36 WILD-TYPE
  R0              14                65
  R1               9                41
  R2               0                 4
  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"
D12V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD36 MUTATED       0                         0    24
  ANKRD36 WILD-TYPE     9                         5   104
D12V14, multiclass
                           clus
vv                          ANKRD36 MUTATED ANKRD36 WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  24               104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
                   cls
clus                 0  1
  ANKRD36 MUTATED    1 18
  ANKRD36 WILD-TYPE  4 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD36 MUTATED      1   18
  ANKRD36 WILD-TYPE    4   87
                        clus
vv                       ANKRD36 MUTATED ANKRD36 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              18                87
[1] 2 2
[1] FALSE

Clustering(13) Variable = RFX1 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2             0  1
  RFX1 MUTATED   11 13
  RFX1 WILD-TYPE 57 63
  RFX1 MUTATED RFX1 WILD-TYPE 
            24            120 
  RFX1 MUTATED RFX1 WILD-TYPE 
            13             63 
$`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-HV-A7OL TCGA-HZ-A49G 
        7.66        12.66        15.55         1.02         8.28        21.70 
TCGA-HZ-A77O TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7887 TCGA-IB-7888 
        5.26         4.77        15.35        19.82         3.62        43.79 
TCGA-IB-8126 TCGA-IB-A6UF TCGA-IB-AAUO TCGA-IB-AAUP TCGA-M8-A5N4 TCGA-Z5-AAPL 
        2.47        21.90         7.86        14.17        19.20        15.35 

$`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        42.31 
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        58.98        43.50         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        16.37         0.03         7.50        12.53        34.82 
TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-8124 TCGA-H6-A45N TCGA-HV-A5A3 
       23.54         4.04         5.03        12.89        13.84         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 
        7.63         9.50        66.94        30.25        17.49        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        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 
       19.82        12.95        49.38        21.90        23.80        41.33 
TCGA-IB-7886 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
        4.04        15.81        19.66        21.30         3.85        15.98 
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-AAUQ 
        1.35         8.22        15.88         0.26         4.73         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-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       10.29         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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 

  RFX1 MUTATED RFX1 WILD-TYPE 
          1.02           0.03 
  RFX1 MUTATED RFX1 WILD-TYPE 
         43.79          75.12 
  RFX1 MUTATED RFX1 WILD-TYPE 
        13.415         14.435 
[1] "1.0 - 43.8 (13.4)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.4"
D13V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RFX1 MUTATED          0        0         6        17         1        0
  RFX1 WILD-TYPE        3        8        17        86         3        4
D13V3, multiclass
           clus
vv          RFX1 MUTATED RFX1 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            6             17
  STAGE IIB           17             86
  STAGE III            1              3
  STAGE IV             0              4
[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    21
  RFX1 WILD-TYPE   4  13   104
D13V4, multiclass
       clus
vv      RFX1 MUTATED RFX1 WILD-TYPE
  T1               0              4
  T2               3             13
  T3+T4           21            104
[1] 3 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
  RFX1 MUTATED    6 18
  RFX1 WILD-TYPE 31 90
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED      6   18
  RFX1 WILD-TYPE   31   90
   clus
vv  RFX1 MUTATED RFX1 WILD-TYPE
  0            6             31
  1           18             90
[1] 2 2
[1] FALSE
D13V6, binary
                cls
clus              0  1
  RFX1 MUTATED   17  0
  RFX1 WILD-TYPE 49  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED     17    0
  RFX1 WILD-TYPE   49    4
   clus
vv  RFX1 MUTATED RFX1 WILD-TYPE
  0           17             49
  1            0              4
[1] 2 2
[1] FALSE
D13V7, binary
                cls
clus              0  1
  RFX1 MUTATED   13 11
  RFX1 WILD-TYPE 54 68
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED     13   11
  RFX1 WILD-TYPE   54   68
        clus
vv       RFX1 MUTATED RFX1 WILD-TYPE
  FEMALE           13             54
  MALE             11             68
[1] 2 2
[1] FALSE
D13V8, binary
                cls
clus              0  1
  RFX1 MUTATED   16  6
  RFX1 WILD-TYPE 78 30
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED     16    6
  RFX1 WILD-TYPE   78   30
     clus
vv    RFX1 MUTATED RFX1 WILD-TYPE
  NO            16             78
  YES            6             30
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RFX1 MUTATED                                    22
  RFX1 WILD-TYPE                                 108
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RFX1 MUTATED                                       2
  RFX1 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RFX1 MUTATED                                                  0
  RFX1 WILD-TYPE                                                2
D13V9, multiclass
                                                  clus
vv                                                 RFX1 MUTATED RFX1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        22            108
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             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"
D13V10, continuous
D13V11, continuous
                vv
clus             R0 R1 R2 RX
  RFX1 MUTATED    9 13  1  0
  RFX1 WILD-TYPE 70 37  3  3
D13V12, multiclass
    clus
vv   RFX1 MUTATED RFX1 WILD-TYPE
  R0            9             70
  R1           13             37
  R2            1              3
  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"
D13V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RFX1 MUTATED       1                         1    20
  RFX1 WILD-TYPE     8                         4   108
D13V14, multiclass
                           clus
vv                          RFX1 MUTATED RFX1 WILD-TYPE
  ASIAN                                1              8
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                               20            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"
D13V15, binary
                cls
clus              0  1
  RFX1 MUTATED    0 16
  RFX1 WILD-TYPE  5 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  RFX1 MUTATED      0   16
  RFX1 WILD-TYPE    5   89
                        clus
vv                       RFX1 MUTATED RFX1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           16             89
[1] 2 2
[1] FALSE

Clustering(14) Variable = TYRO3 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2              0  1
  TYRO3 MUTATED    7  7
  TYRO3 WILD-TYPE 61 69
  TYRO3 MUTATED TYRO3 WILD-TYPE 
             14             130 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              7              69 
$`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         0.03 
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 TCGA-XN-A8T3 
       16.80        31.27 

$`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        42.31        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IZ 
       20.84         7.36        24.26        33.57        15.06        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       24.43        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        12.66        16.37         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A6UF TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 
        7.20        15.12        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-A77E 
       24.23        17.26        23.08        22.85        39.98        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 
        0.39        13.81        12.99        12.03        16.37        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  TYRO3 MUTATED TYRO3 WILD-TYPE 
           0.03            0.13 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
          34.09           75.12 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
         14.875          14.285 
[1] "0.0 - 34.1 (14.9)" "0.1 - 75.1 (14.3)"
[1] "hr=" "1.1"
D14V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TYRO3 MUTATED          1        1         1        10         0        1
  TYRO3 WILD-TYPE        2        7        22        93         4        3
D14V3, multiclass
           clus
vv          TYRO3 MUTATED TYRO3 WILD-TYPE
  STAGE IA              1               2
  STAGE IB              1               7
  STAGE IIA             1              22
  STAGE IIB            10              93
  STAGE III             0               4
  STAGE IV              1               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
  TYRO3 MUTATED     1   3    10
  TYRO3 WILD-TYPE   3  13   115
D14V4, multiclass
       clus
vv      TYRO3 MUTATED TYRO3 WILD-TYPE
  T1                1               3
  T2                3              13
  T3+T4            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"
D14V5, binary
                 cls
clus               0  1
  TYRO3 MUTATED    3 11
  TYRO3 WILD-TYPE 34 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      3   11
  TYRO3 WILD-TYPE   34   97
   clus
vv  TYRO3 MUTATED TYRO3 WILD-TYPE
  0             3              34
  1            11              97
[1] 2 2
[1] FALSE
D14V6, binary
                 cls
clus               0  1
  TYRO3 MUTATED    8  1
  TYRO3 WILD-TYPE 58  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      8    1
  TYRO3 WILD-TYPE   58    3
   clus
vv  TYRO3 MUTATED TYRO3 WILD-TYPE
  0             8              58
  1             1               3
[1] 2 2
[1] FALSE
D14V7, binary
                 cls
clus               0  1
  TYRO3 MUTATED    5  9
  TYRO3 WILD-TYPE 62 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      5    9
  TYRO3 WILD-TYPE   62   70
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  FEMALE             5              62
  MALE               9              70
[1] 2 2
[1] FALSE
D14V8, binary
                 cls
clus               0  1
  TYRO3 MUTATED    7  5
  TYRO3 WILD-TYPE 87 31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      7    5
  TYRO3 WILD-TYPE   87   31
     clus
vv    TYRO3 MUTATED TYRO3 WILD-TYPE
  NO              7              87
  YES             5              31
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TYRO3 MUTATED                                    13
  TYRO3 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TYRO3 MUTATED                                       1
  TYRO3 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TYRO3 MUTATED                                                  0
  TYRO3 WILD-TYPE                                                2
D14V9, multiclass
                                                  clus
vv                                                 TYRO3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 TYRO3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D14V10, continuous
D14V11, continuous
                 vv
clus              R0 R1 R2 RX
  TYRO3 MUTATED    9  4  0  0
  TYRO3 WILD-TYPE 70 46  4  3
D14V12, multiclass
    clus
vv   TYRO3 MUTATED TYRO3 WILD-TYPE
  R0             9              70
  R1             4              46
  R2             0               4
  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"
D14V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TYRO3 MUTATED       0                         0    14
  TYRO3 WILD-TYPE     9                         5   114
D14V14, multiclass
                           clus
vv                          TYRO3 MUTATED TYRO3 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                14             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"
D14V15, binary
                 cls
clus               0  1
  TYRO3 MUTATED    1  9
  TYRO3 WILD-TYPE  4 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      1    9
  TYRO3 WILD-TYPE    4   96
                        clus
vv                       TYRO3 MUTATED TYRO3 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             9              96
[1] 2 2
[1] FALSE

Clustering(15) Variable = NCOA3 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2              0  1
  NCOA3 MUTATED    6  8
  NCOA3 WILD-TYPE 62 68
  NCOA3 MUTATED NCOA3 WILD-TYPE 
             14             130 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              8              68 
$`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-HZ-A9TJ TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-A6UG TCGA-LB-A8F3 
       12.43        19.82        15.35        19.82         1.35        12.46 
TCGA-M8-A5N4 TCGA-S4-A8RO 
       19.20        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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 TCGA-F2-A44G 
       34.09        10.13        24.43        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        12.66        16.37 
TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
        0.03         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HV-A5A3 TCGA-HV-A5A4 
        5.03         1.02        12.89        13.84         4.21         7.63 
TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7922 
        9.50        66.94         8.28        30.25        17.49         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
        9.83        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-7885 
       12.95        49.38         4.77        21.90        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-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-A9Q5 TCGA-OE-A75W 
        7.40         9.44         8.05        12.92        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        24.23 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  NCOA3 MUTATED NCOA3 WILD-TYPE 
           1.35            0.03 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
          71.74           75.12 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
         16.455          13.990 
[1] "1.4 - 71.7 (16.5)" "0.0 - 75.1 (14.0)"
[1] "hr=" "1"  
D15V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NCOA3 MUTATED          0        0         5         8         0        1
  NCOA3 WILD-TYPE        3        8        18        95         4        3
D15V3, multiclass
           clus
vv          NCOA3 MUTATED NCOA3 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             5              18
  STAGE IIB             8              95
  STAGE III             0               4
  STAGE IV              1               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    14
  NCOA3 WILD-TYPE   4  16   111
D15V4, multiclass
       clus
vv      NCOA3 MUTATED NCOA3 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4            14             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"
D15V5, binary
                 cls
clus                0   1
  NCOA3 MUTATED     6   8
  NCOA3 WILD-TYPE  31 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      6    8
  NCOA3 WILD-TYPE   31  100
   clus
vv  NCOA3 MUTATED NCOA3 WILD-TYPE
  0             6              31
  1             8             100
[1] 2 2
[1] FALSE
D15V6, binary
                 cls
clus               0  1
  NCOA3 MUTATED    8  1
  NCOA3 WILD-TYPE 58  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      8    1
  NCOA3 WILD-TYPE   58    3
   clus
vv  NCOA3 MUTATED NCOA3 WILD-TYPE
  0             8              58
  1             1               3
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus               0  1
  NCOA3 MUTATED    7  7
  NCOA3 WILD-TYPE 60 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      7    7
  NCOA3 WILD-TYPE   60   72
        clus
vv       NCOA3 MUTATED NCOA3 WILD-TYPE
  FEMALE             7              60
  MALE               7              72
[1] 2 2
[1] FALSE
D15V8, binary
                 cls
clus               0  1
  NCOA3 MUTATED    7  5
  NCOA3 WILD-TYPE 87 31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      7    5
  NCOA3 WILD-TYPE   87   31
     clus
vv    NCOA3 MUTATED NCOA3 WILD-TYPE
  NO              7              87
  YES             5              31
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NCOA3 MUTATED                                    13
  NCOA3 WILD-TYPE                                 117
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NCOA3 MUTATED                                       1
  NCOA3 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NCOA3 MUTATED                                                  0
  NCOA3 WILD-TYPE                                                2
D15V9, multiclass
                                                  clus
vv                                                 NCOA3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NCOA3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D15V10, continuous
D15V11, continuous
                 vv
clus              R0 R1 R2 RX
  NCOA3 MUTATED    4  9  0  0
  NCOA3 WILD-TYPE 75 41  4  3
D15V12, multiclass
    clus
vv   NCOA3 MUTATED NCOA3 WILD-TYPE
  R0             4              75
  R1             9              41
  R2             0               4
  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"
D15V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NCOA3 MUTATED       0                         1    11
  NCOA3 WILD-TYPE     9                         4   117
D15V14, multiclass
                           clus
vv                          NCOA3 MUTATED NCOA3 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                11             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"
D15V15, binary
                 cls
clus               0  1
  NCOA3 MUTATED    1  9
  NCOA3 WILD-TYPE  4 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      1    9
  NCOA3 WILD-TYPE    4   96
                        clus
vv                       NCOA3 MUTATED NCOA3 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             9              96
[1] 2 2
[1] FALSE

Clustering(16) Variable = GPR6 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2             0  1
  GPR6 MUTATED    5  6
  GPR6 WILD-TYPE 63 70
  GPR6 MUTATED GPR6 WILD-TYPE 
            11            133 
  GPR6 MUTATED GPR6 WILD-TYPE 
             6             70 
$`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        15.35 

$`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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-A44G 
       34.09        10.13        24.43        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         3.95         9.83        12.43        14.93 
TCGA-HZ-8636 TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
       17.92        16.14        10.13         6.38        21.60         5.26 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-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-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        24.23        17.26 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  GPR6 MUTATED GPR6 WILD-TYPE 
          2.17           0.03 
  GPR6 MUTATED GPR6 WILD-TYPE 
         23.80          75.12 
  GPR6 MUTATED GPR6 WILD-TYPE 
         15.35          13.84 
[1] "2.2 - 23.8 (15.3)" "0.0 - 75.1 (13.8)"
[1] "hr=" "1.1"
D16V2, 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        3        8        20        94         4        4
D16V3, multiclass
           clus
vv          GPR6 MUTATED GPR6 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            3             20
  STAGE IIB            9             94
  STAGE III            0              4
  STAGE IV             0              4
[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   4  15   114
D16V4, multiclass
       clus
vv      GPR6 MUTATED GPR6 WILD-TYPE
  T1               0              4
  T2               1             15
  T3+T4           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"
D16V5, binary
                cls
clus              0  1
  GPR6 MUTATED    3  9
  GPR6 WILD-TYPE 34 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR6 MUTATED      3    9
  GPR6 WILD-TYPE   34   99
   clus
vv  GPR6 MUTATED GPR6 WILD-TYPE
  0            3             34
  1            9             99
[1] 2 2
[1] FALSE
D16V6, binary
                cls
clus              0  1
  GPR6 MUTATED    8  0
  GPR6 WILD-TYPE 58  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR6 MUTATED      8    0
  GPR6 WILD-TYPE   58    4
   clus
vv  GPR6 MUTATED GPR6 WILD-TYPE
  0            8             58
  1            0              4
[1] 2 2
[1] FALSE
D16V7, binary
                cls
clus              0  1
  GPR6 MUTATED    8  4
  GPR6 WILD-TYPE 59 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR6 MUTATED      8    4
  GPR6 WILD-TYPE   59   75
        clus
vv       GPR6 MUTATED GPR6 WILD-TYPE
  FEMALE            8             59
  MALE              4             75
[1] 2 2
[1] FALSE
D16V8, binary
                cls
clus              0  1
  GPR6 MUTATED    8  3
  GPR6 WILD-TYPE 86 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR6 MUTATED      8    3
  GPR6 WILD-TYPE   86   33
     clus
vv    GPR6 MUTATED GPR6 WILD-TYPE
  NO             8             86
  YES            3             33
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPR6 MUTATED                                    10
  GPR6 WILD-TYPE                                 120
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPR6 MUTATED                                       2
  GPR6 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPR6 MUTATED                                                  0
  GPR6 WILD-TYPE                                                2
D16V9, multiclass
                                                  clus
vv                                                 GPR6 MUTATED GPR6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        10            120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             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"
D16V10, continuous
D16V11, continuous
                vv
clus             R0 R1 R2 RX
  GPR6 MUTATED    9  3  0  0
  GPR6 WILD-TYPE 70 47  4  3
D16V12, multiclass
    clus
vv   GPR6 MUTATED GPR6 WILD-TYPE
  R0            9             70
  R1            3             47
  R2            0              4
  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"
D16V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR6 MUTATED       1                         0    11
  GPR6 WILD-TYPE     8                         5   117
D16V14, multiclass
                           clus
vv                          GPR6 MUTATED GPR6 WILD-TYPE
  ASIAN                                1              8
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               11            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"
D16V15, binary
                cls
clus              0  1
  GPR6 MUTATED    1  7
  GPR6 WILD-TYPE  4 98
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPR6 MUTATED      1    7
  GPR6 WILD-TYPE    4   98
                        clus
vv                       GPR6 MUTATED GPR6 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            7             98
[1] 2 2
[1] FALSE

Clustering(17) Variable = LZTS1 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2              0  1
  LZTS1 MUTATED    4  6
  LZTS1 WILD-TYPE 64 70
  LZTS1 MUTATED LZTS1 WILD-TYPE 
             10             134 
  LZTS1 MUTATED LZTS1 WILD-TYPE 
              6              70 
$`LZTS1 MUTATED`
TCGA-2J-AAB9 TCGA-2J-AABO TCGA-HV-A5A5 TCGA-HV-A7OL TCGA-HZ-7926 TCGA-HZ-A49I 
       20.61        14.47         9.50         8.28        17.03        10.13 
TCGA-HZ-A4BH TCGA-IB-7651 TCGA-IB-7893 TCGA-IB-7897 
        6.38        19.82         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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 TCGA-HV-AA8V TCGA-HV-AA8X 
       13.84         4.21         7.63        66.94        30.25        17.49 
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        19.59 
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-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
       16.14        21.60         5.26        10.85         1.08         0.23 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  LZTS1 MUTATED LZTS1 WILD-TYPE 
           3.85            0.03 
  LZTS1 MUTATED LZTS1 WILD-TYPE 
          20.61           75.12 
  LZTS1 MUTATED LZTS1 WILD-TYPE 
         12.300          14.285 
[1] "3.9 - 20.6 (12.3)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.6"
D17V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  LZTS1 MUTATED          0        0         2         8         0        0
  LZTS1 WILD-TYPE        3        8        21        95         4        4
D17V3, multiclass
           clus
vv          LZTS1 MUTATED LZTS1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             2              21
  STAGE IIB             8              95
  STAGE III             0               4
  STAGE IV              0               4
[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    10
  LZTS1 WILD-TYPE   4  16   115
D17V4, multiclass
       clus
vv      LZTS1 MUTATED LZTS1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4            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"
D17V5, binary
                 cls
clus                0   1
  LZTS1 MUTATED     2   8
  LZTS1 WILD-TYPE  35 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTS1 MUTATED      2    8
  LZTS1 WILD-TYPE   35  100
   clus
vv  LZTS1 MUTATED LZTS1 WILD-TYPE
  0             2              35
  1             8             100
[1] 2 2
[1] FALSE
D17V6, binary
                 cls
clus               0  1
  LZTS1 MUTATED    6  0
  LZTS1 WILD-TYPE 60  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTS1 MUTATED      6    0
  LZTS1 WILD-TYPE   60    4
   clus
vv  LZTS1 MUTATED LZTS1 WILD-TYPE
  0             6              60
  1             0               4
[1] 2 2
[1] FALSE
D17V7, binary
                 cls
clus               0  1
  LZTS1 MUTATED    4  6
  LZTS1 WILD-TYPE 63 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTS1 MUTATED      4    6
  LZTS1 WILD-TYPE   63   73
        clus
vv       LZTS1 MUTATED LZTS1 WILD-TYPE
  FEMALE             4              63
  MALE               6              73
[1] 2 2
[1] FALSE
D17V8, binary
                 cls
clus               0  1
  LZTS1 MUTATED    5  3
  LZTS1 WILD-TYPE 89 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTS1 MUTATED      5    3
  LZTS1 WILD-TYPE   89   33
     clus
vv    LZTS1 MUTATED LZTS1 WILD-TYPE
  NO              5              89
  YES             3              33
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LZTS1 MUTATED                                    10
  LZTS1 WILD-TYPE                                 120
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LZTS1 MUTATED                                       0
  LZTS1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LZTS1 MUTATED                                                  0
  LZTS1 WILD-TYPE                                                2
D17V9, multiclass
                                                  clus
vv                                                 LZTS1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 LZTS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          120
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D17V10, continuous
[1] "Remove cluster labels:" "LZTS1 MUTATED"         
clus
  LZTS1 MUTATED LZTS1 WILD-TYPE 
              2              48 
     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-HV-AA8V 
"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-7887 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
D17V11, continuous
[1] "Remove cluster labels:" "LZTS1 MUTATED"         
clus
  LZTS1 MUTATED LZTS1 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"LZTS1 WILD-TYPE" "LZTS1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  LZTS1 MUTATED    5  2  1  1
  LZTS1 WILD-TYPE 74 48  3  2
D17V12, multiclass
    clus
vv   LZTS1 MUTATED LZTS1 WILD-TYPE
  R0             5              74
  R1             2              48
  R2             1               3
  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"
D17V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LZTS1 MUTATED       2                         1     7
  LZTS1 WILD-TYPE     7                         4   121
D17V14, multiclass
                           clus
vv                          LZTS1 MUTATED LZTS1 WILD-TYPE
  ASIAN                                 2               7
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 7             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"
D17V15, binary
                 cls
clus                0   1
  LZTS1 MUTATED     0   5
  LZTS1 WILD-TYPE   5 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LZTS1 MUTATED      0    5
  LZTS1 WILD-TYPE    5  100
                        clus
vv                       LZTS1 MUTATED LZTS1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             100
[1] 2 2
[1] FALSE

Clustering(18) Variable = KRAS MUTATION ANALYSIS
D18V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   54 67
  KRAS WILD-TYPE 14  9
  KRAS MUTATED KRAS WILD-TYPE 
           121             23 
  KRAS MUTATED KRAS WILD-TYPE 
            67              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        42.31        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 
       43.50        20.84         7.36        24.26        33.57        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        12.66        16.37         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-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
       13.84         4.21         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        1.08         0.23        19.82        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-7889 TCGA-IB-7890 TCGA-IB-7893 TCGA-IB-8127 TCGA-IB-A5SO 
        3.62        15.81        19.66         3.85        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-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-AAUU TCGA-LB-A9Q5 TCGA-M8-A5N4 TCGA-OE-A75W 
       11.11         7.40         8.05        10.29        19.20         8.78 
TCGA-PZ-A5RE TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO 
       15.45         3.12        15.32         9.40        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUI 
       23.08        22.85        16.80         0.39        13.81        12.03 
TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

$`KRAS WILD-TYPE`
TCGA-2J-AABA TCGA-3A-A9I5 TCGA-3A-A9J0 TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A4P6 
       19.96        58.98        24.43        19.27         5.88        11.93 
TCGA-FB-A78T TCGA-FB-AAPY TCGA-HV-A5A4 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-IB-7888 
        0.03        34.82         7.63        12.43        14.93        43.79 
TCGA-IB-7891 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SQ TCGA-IB-AAUT TCGA-LB-A7SX 
       21.30        15.98         2.47         7.20         9.44        12.92 
TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-US-A776 TCGA-US-A77E TCGA-XD-AAUH 
       12.46        13.68        39.98        14.14        12.99 

  KRAS MUTATED KRAS WILD-TYPE 
          0.13           0.03 
  KRAS MUTATED KRAS WILD-TYPE 
         75.12          58.98 
  KRAS MUTATED KRAS WILD-TYPE 
         14.47          13.68 
[1] "0.1 - 75.1 (14.5)" "0.0 - 59.0 (13.7)"
[1] "hr=" "1.5"
D18V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KRAS MUTATED          2        7        18        89         3        4
  KRAS WILD-TYPE        1        1         5        14         1        0
D18V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE IA             2              1
  STAGE IB             7              1
  STAGE IIA           18              5
  STAGE IIB           89             14
  STAGE III            3              1
  STAGE IV             4              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  13   107
  KRAS WILD-TYPE   1   3    18
D18V4, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  T1               3              1
  T2              13              3
  T3+T4          107             18
[1] 3 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
  KRAS MUTATED   29 93
  KRAS WILD-TYPE  8 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     29   93
  KRAS WILD-TYPE    8   15
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           29              8
  1           93             15
[1] 2 2
[1] FALSE
D18V6, binary
                cls
clus              0  1
  KRAS MUTATED   56  4
  KRAS WILD-TYPE 10  0
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     56    4
  KRAS WILD-TYPE   10    0
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0           56             10
  1            4              0
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus              0  1
  KRAS MUTATED   55 68
  KRAS WILD-TYPE 12 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     55   68
  KRAS WILD-TYPE   12   11
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           55             12
  MALE             68             11
[1] 2 2
[1] FALSE
D18V8, binary
                cls
clus              0  1
  KRAS MUTATED   82 28
  KRAS WILD-TYPE 12  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     82   28
  KRAS WILD-TYPE   12    8
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO            82             12
  YES           28              8
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KRAS MUTATED                                   111
  KRAS WILD-TYPE                                  19
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KRAS MUTATED                                      11
  KRAS WILD-TYPE                                     2
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KRAS MUTATED                                                  0
  KRAS WILD-TYPE                                                2
D18V9, multiclass
                                                  clus
vv                                                 KRAS MUTATED KRAS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       111             19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      11              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"
D18V10, continuous
D18V11, continuous
                vv
clus             R0 R1 R2 RX
  KRAS MUTATED   65 44  3  3
  KRAS WILD-TYPE 14  6  1  0
D18V12, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           65             14
  R1           44              6
  R2            3              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"
D18V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       8                         2   109
  KRAS WILD-TYPE     1                         3    19
D18V14, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                8              1
  BLACK OR AFRICAN AMERICAN            2              3
  WHITE                              109             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"
D18V15, binary
                cls
clus              0  1
  KRAS MUTATED    5 84
  KRAS WILD-TYPE  0 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      5   84
  KRAS WILD-TYPE    0   21
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                5              0
  NOT HISPANIC OR LATINO           84             21
[1] 2 2
[1] FALSE

Clustering(19) Variable = ZMIZ2 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2              0  1
  ZMIZ2 MUTATED    5  7
  ZMIZ2 WILD-TYPE 63 69
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
             12             132 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
              7              69 
$`ZMIZ2 MUTATED`
TCGA-2J-AABH TCGA-F2-A44G TCGA-FB-A545 TCGA-HZ-8519 TCGA-IB-7644 TCGA-IB-7651 
       42.31         7.66        12.66        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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 
       16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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-8636 
       12.03        19.59         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-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        19.82        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-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00        15.85         7.20        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL 
       39.98        14.14        13.81        12.99        12.03        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
           0.39            0.03 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
          42.31           75.12 
  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE 
         15.025          14.155 
[1] "0.4 - 42.3 (15.0)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.3"
D19V2, 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        2        8        22        94         4        3
D19V3, multiclass
           clus
vv          ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  STAGE IA              1               2
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             9              94
  STAGE III             0               4
  STAGE IV              1               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
  ZMIZ2 MUTATED     1   0    11
  ZMIZ2 WILD-TYPE   3  16   114
D19V4, multiclass
       clus
vv      ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  T1                1               3
  T2                0              16
  T3+T4            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"
D19V5, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    2 10
  ZMIZ2 WILD-TYPE 35 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      2   10
  ZMIZ2 WILD-TYPE   35   98
   clus
vv  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  0             2              35
  1            10              98
[1] 2 2
[1] FALSE
D19V6, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    8  1
  ZMIZ2 WILD-TYPE 58  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      8    1
  ZMIZ2 WILD-TYPE   58    3
   clus
vv  ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  0             8              58
  1             1               3
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    7  5
  ZMIZ2 WILD-TYPE 60 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      7    5
  ZMIZ2 WILD-TYPE   60   74
        clus
vv       ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  FEMALE             7              60
  MALE               5              74
[1] 2 2
[1] FALSE
D19V8, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    8  3
  ZMIZ2 WILD-TYPE 86 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      8    3
  ZMIZ2 WILD-TYPE   86   33
     clus
vv    ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  NO              8              86
  YES             3              33
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMIZ2 MUTATED                                    10
  ZMIZ2 WILD-TYPE                                 120
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMIZ2 MUTATED                                       2
  ZMIZ2 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMIZ2 MUTATED                                                  0
  ZMIZ2 WILD-TYPE                                                2
D19V9, 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                          120
  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"
D19V10, continuous
D19V11, continuous
                 vv
clus              R0 R1 R2 RX
  ZMIZ2 MUTATED    7  4  0  0
  ZMIZ2 WILD-TYPE 72 46  4  3
D19V12, multiclass
    clus
vv   ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  R0             7              72
  R1             4              46
  R2             0               4
  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"
D19V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMIZ2 MUTATED       0                         0    12
  ZMIZ2 WILD-TYPE     9                         5   116
D19V14, multiclass
                           clus
vv                          ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                12             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"
D19V15, binary
                 cls
clus               0  1
  ZMIZ2 MUTATED    0 11
  ZMIZ2 WILD-TYPE  5 94
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ2 MUTATED      0   11
  ZMIZ2 WILD-TYPE    5   94
                        clus
vv                       ZMIZ2 MUTATED ZMIZ2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO            11              94
[1] 2 2
[1] FALSE

Clustering(20) Variable = IRS4 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2             0  1
  IRS4 MUTATED   11  4
  IRS4 WILD-TYPE 57 72
  IRS4 MUTATED IRS4 WILD-TYPE 
            15            129 
  IRS4 MUTATED IRS4 WILD-TYPE 
             4             72 
$`IRS4 MUTATED`
TCGA-2J-AAB4 TCGA-2J-AABU TCGA-F2-A8YN TCGA-FB-AAPS TCGA-HV-A5A4 TCGA-HV-A5A5 
       23.97         9.11        17.00         7.50         7.63         9.50 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-IB-7646 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7887 
       21.70        16.14         4.77        19.82        23.80         3.62 
TCGA-IB-AAUM TCGA-S4-A8RO TCGA-Z5-AAPL 
        0.26        17.26        15.35 

$`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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
       16.37         0.03        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-H6-A45N TCGA-HV-A5A3 
        4.04         5.03         1.02        12.89        13.84         4.21 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49I TCGA-HZ-A4BH 
        9.83        12.43        14.93        17.92        10.13         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       11.51        12.76        66.28 

  IRS4 MUTATED IRS4 WILD-TYPE 
          0.26           0.03 
  IRS4 MUTATED IRS4 WILD-TYPE 
         23.97          75.12 
  IRS4 MUTATED IRS4 WILD-TYPE 
         15.35          14.17 
[1] "0.3 - 24.0 (15.3)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.8"
D20V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  IRS4 MUTATED          0        0         3        13         0        0
  IRS4 WILD-TYPE        3        8        20        90         4        4
D20V3, multiclass
           clus
vv          IRS4 MUTATED IRS4 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            3             20
  STAGE IIB           13             90
  STAGE III            0              4
  STAGE IV             0              4
[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    12
  IRS4 WILD-TYPE   4  12   113
D20V4, multiclass
       clus
vv      IRS4 MUTATED IRS4 WILD-TYPE
  T1               0              4
  T2               4             12
  T3+T4           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"
D20V5, binary
                cls
clus              0  1
  IRS4 MUTATED    3 13
  IRS4 WILD-TYPE 34 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      3   13
  IRS4 WILD-TYPE   34   95
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0            3             34
  1           13             95
[1] 2 2
[1] FALSE
D20V6, binary
                cls
clus              0  1
  IRS4 MUTATED   10  0
  IRS4 WILD-TYPE 56  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     10    0
  IRS4 WILD-TYPE   56    4
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0           10             56
  1            0              4
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus              0  1
  IRS4 MUTATED   11  5
  IRS4 WILD-TYPE 56 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     11    5
  IRS4 WILD-TYPE   56   74
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE           11             56
  MALE              5             74
[1] 2 2
[1] FALSE
D20V8, binary
                cls
clus              0  1
  IRS4 MUTATED   12  3
  IRS4 WILD-TYPE 82 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     12    3
  IRS4 WILD-TYPE   82   33
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO            12             82
  YES            3             33
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IRS4 MUTATED                                    15
  IRS4 WILD-TYPE                                 115
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IRS4 MUTATED                                       1
  IRS4 WILD-TYPE                                    12
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IRS4 MUTATED                                                  0
  IRS4 WILD-TYPE                                                2
D20V9, multiclass
                                                  clus
vv                                                 IRS4 MUTATED IRS4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        15            115
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             12
  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"
D20V10, continuous
D20V11, continuous
[1] "Remove cluster labels:" "IRS4 MUTATED"          
clus
  IRS4 MUTATED IRS4 WILD-TYPE 
             2             38 
    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-XN-A8T5     TCGA-YY-A8LH 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  IRS4 MUTATED    8  6  0  0
  IRS4 WILD-TYPE 71 44  4  3
D20V12, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  R0            8             71
  R1            6             44
  R2            0              4
  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"
D20V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED       3                         0    13
  IRS4 WILD-TYPE     6                         5   115
D20V14, multiclass
                           clus
vv                          IRS4 MUTATED IRS4 WILD-TYPE
  ASIAN                                3              6
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                               13            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"
D20V15, binary
                cls
clus              0  1
  IRS4 MUTATED    1 11
  IRS4 WILD-TYPE  4 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      1   11
  IRS4 WILD-TYPE    4   94
                        clus
vv                       IRS4 MUTATED IRS4 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO           11             94
[1] 2 2
[1] FALSE

Clustering(21) Variable = SIK3 MUTATION ANALYSIS
D21V1, survival
                sevent
clus2             0  1
  SIK3 MUTATED    6  7
  SIK3 WILD-TYPE 62 69
  SIK3 MUTATED SIK3 WILD-TYPE 
            13            131 
  SIK3 MUTATED SIK3 WILD-TYPE 
             7             69 
$`SIK3 MUTATED`
TCGA-2J-AABU TCGA-FB-A4P6 TCGA-HV-A5A5 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-IB-7649 
        9.11        11.93         9.50        17.03        12.03        15.35 
TCGA-IB-7888 TCGA-IB-7890 TCGA-IB-A5SP TCGA-IB-A6UF TCGA-LB-A8F3 TCGA-Q3-A5QY 
       43.79        19.66        15.85        21.90        12.46        13.68 
TCGA-US-A774 
       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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
       13.84         4.21         7.63        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8003 
       17.49        19.50         0.13        20.19        23.21        19.59 
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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        1.08         0.23        19.82        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-7889 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       15.81        21.30         3.85        15.98         2.47        17.16 
TCGA-IB-A5SO TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX 
       12.00         7.20        15.12        20.88         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-A9Q5 
       11.11         7.40         9.44         8.05        12.92        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-A776 TCGA-US-A779 TCGA-US-A77E 
       24.23        17.26        23.08        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
        0.39        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  SIK3 MUTATED SIK3 WILD-TYPE 
          9.11           0.03 
  SIK3 MUTATED SIK3 WILD-TYPE 
         43.79          75.12 
  SIK3 MUTATED SIK3 WILD-TYPE 
         15.35          14.17 
[1] "9.1 - 43.8 (15.3)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1"  
D21V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SIK3 MUTATED          0        1         3         9         0        0
  SIK3 WILD-TYPE        3        7        20        94         4        4
D21V3, multiclass
           clus
vv          SIK3 MUTATED SIK3 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             1              7
  STAGE IIA            3             20
  STAGE IIB            9             94
  STAGE III            0              4
  STAGE IV             0              4
[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    12
  SIK3 WILD-TYPE   4  15   113
D21V4, multiclass
       clus
vv      SIK3 MUTATED SIK3 WILD-TYPE
  T1               0              4
  T2               1             15
  T3+T4           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"
D21V5, binary
                cls
clus              0  1
  SIK3 MUTATED    4  9
  SIK3 WILD-TYPE 33 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK3 MUTATED      4    9
  SIK3 WILD-TYPE   33   99
   clus
vv  SIK3 MUTATED SIK3 WILD-TYPE
  0            4             33
  1            9             99
[1] 2 2
[1] FALSE
D21V6, binary
                cls
clus              0  1
  SIK3 MUTATED    7  0
  SIK3 WILD-TYPE 59  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK3 MUTATED      7    0
  SIK3 WILD-TYPE   59    4
   clus
vv  SIK3 MUTATED SIK3 WILD-TYPE
  0            7             59
  1            0              4
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus              0  1
  SIK3 MUTATED    5  8
  SIK3 WILD-TYPE 62 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK3 MUTATED      5    8
  SIK3 WILD-TYPE   62   71
        clus
vv       SIK3 MUTATED SIK3 WILD-TYPE
  FEMALE            5             62
  MALE              8             71
[1] 2 2
[1] FALSE
D21V8, binary
                cls
clus              0  1
  SIK3 MUTATED   10  2
  SIK3 WILD-TYPE 84 34
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK3 MUTATED     10    2
  SIK3 WILD-TYPE   84   34
     clus
vv    SIK3 MUTATED SIK3 WILD-TYPE
  NO            10             84
  YES            2             34
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SIK3 MUTATED                                    13
  SIK3 WILD-TYPE                                 117
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SIK3 MUTATED                                       0
  SIK3 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SIK3 MUTATED                                                  0
  SIK3 WILD-TYPE                                                2
D21V9, multiclass
                                                  clus
vv                                                 SIK3 MUTATED SIK3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        13            117
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D21V10, continuous
D21V11, continuous
                vv
clus             R0 R1 R2 RX
  SIK3 MUTATED    7  3  0  1
  SIK3 WILD-TYPE 72 47  4  2
D21V12, multiclass
    clus
vv   SIK3 MUTATED SIK3 WILD-TYPE
  R0            7             72
  R1            3             47
  R2            0              4
  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"
D21V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SIK3 MUTATED       1                         3     7
  SIK3 WILD-TYPE     8                         2   121
D21V14, multiclass
                           clus
vv                          SIK3 MUTATED SIK3 WILD-TYPE
  ASIAN                                1              8
  BLACK OR AFRICAN AMERICAN            3              2
  WHITE                                7            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"
D21V15, binary
                cls
clus              0  1
  SIK3 MUTATED    0  8
  SIK3 WILD-TYPE  5 97
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIK3 MUTATED      0    8
  SIK3 WILD-TYPE    5   97
                        clus
vv                       SIK3 MUTATED SIK3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            8             97
[1] 2 2
[1] FALSE

Clustering(22) Variable = PABPC1 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2               0  1
  PABPC1 MUTATED    4  5
  PABPC1 WILD-TYPE 64 71
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               9              135 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               5               71 
$`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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-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-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-A8RM 
       15.45        13.68         3.12        15.32         9.40        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
        0.39        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        66.28        15.35 

  PABPC1 MUTATED PABPC1 WILD-TYPE 
            1.35             0.03 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           22.72            75.12 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           12.43            14.93 
[1] "1.4 - 22.7 (12.4)" "0.0 - 75.1 (14.9)"
[1] "hr=" "1.8"
D22V2, 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        3        8        22        97         3        3
D22V3, multiclass
           clus
vv          PABPC1 MUTATED PABPC1 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              6               97
  STAGE III              1                3
  STAGE IV               1                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
  PABPC1 MUTATED     0   0     9
  PABPC1 WILD-TYPE   4  16   116
D22V4, multiclass
       clus
vv      PABPC1 MUTATED PABPC1 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D22V5, binary
                  cls
clus                 0   1
  PABPC1 MUTATED     1   8
  PABPC1 WILD-TYPE  36 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      1    8
  PABPC1 WILD-TYPE   36  100
   clus
vv  PABPC1 MUTATED PABPC1 WILD-TYPE
  0              1               36
  1              8              100
[1] 2 2
[1] FALSE
D22V6, binary
                  cls
clus                0  1
  PABPC1 MUTATED    5  1
  PABPC1 WILD-TYPE 61  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      5    1
  PABPC1 WILD-TYPE   61    3
   clus
vv  PABPC1 MUTATED PABPC1 WILD-TYPE
  0              5               61
  1              1                3
[1] 2 2
[1] FALSE
D22V7, binary
                  cls
clus                0  1
  PABPC1 MUTATED    4  5
  PABPC1 WILD-TYPE 63 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      4    5
  PABPC1 WILD-TYPE   63   74
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  FEMALE              4               63
  MALE                5               74
[1] 2 2
[1] FALSE
D22V8, binary
                  cls
clus                0  1
  PABPC1 MUTATED    6  3
  PABPC1 WILD-TYPE 88 33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      6    3
  PABPC1 WILD-TYPE   88   33
     clus
vv    PABPC1 MUTATED PABPC1 WILD-TYPE
  NO               6               88
  YES              3               33
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PABPC1 MUTATED                                     8
  PABPC1 WILD-TYPE                                 122
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PABPC1 MUTATED                                       0
  PABPC1 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PABPC1 MUTATED                                                  0
  PABPC1 WILD-TYPE                                                2
D22V9, 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                           122
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D22V10, continuous
D22V11, continuous
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PABPC1 MUTATED    2  6  0  0
  PABPC1 WILD-TYPE 77 44  4  3
D22V12, multiclass
    clus
vv   PABPC1 MUTATED PABPC1 WILD-TYPE
  R0              2               77
  R1              6               44
  R2              0                4
  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"
D22V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PABPC1 MUTATED       0                         0     9
  PABPC1 WILD-TYPE     9                         5   119
D22V14, multiclass
                           clus
vv                          PABPC1 MUTATED PABPC1 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  9              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"
D22V15, binary
                  cls
clus                0  1
  PABPC1 MUTATED    0  7
  PABPC1 WILD-TYPE  5 98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      0    7
  PABPC1 WILD-TYPE    5   98
                        clus
vv                       PABPC1 MUTATED PABPC1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               98
[1] 2 2
[1] FALSE

Clustering(23) Variable = RBMX MUTATION ANALYSIS
D23V1, survival
                sevent
clus2             0  1
  RBMX MUTATED    2  3
  RBMX WILD-TYPE 66 73
  RBMX MUTATED RBMX WILD-TYPE 
             5            139 
  RBMX MUTATED RBMX WILD-TYPE 
             3             73 
$`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 
       42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
       17.49         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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       12.03        16.37        31.27        23.67        11.51        66.28 
TCGA-Z5-AAPL 
       15.35 

  RBMX MUTATED RBMX WILD-TYPE 
          4.04           0.03 
  RBMX MUTATED RBMX WILD-TYPE 
         23.97          75.12 
  RBMX MUTATED RBMX WILD-TYPE 
         12.76          14.40 
[1] "4.0 - 24.0 (12.8)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.3"
D23V2, 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        3        8        22       100         3        4
D23V3, multiclass
           clus
vv          RBMX MUTATED RBMX WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            1             22
  STAGE IIB            3            100
  STAGE III            1              3
  STAGE IV             0              4
[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   4  15   121
D23V4, multiclass
       clus
vv      RBMX MUTATED RBMX WILD-TYPE
  T1               0              4
  T2               1             15
  T3+T4            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"
D23V5, binary
                cls
clus               0   1
  RBMX MUTATED     1   4
  RBMX WILD-TYPE  36 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      1    4
  RBMX WILD-TYPE   36  104
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0            1             36
  1            4            104
[1] 2 2
[1] FALSE
D23V6, binary
                cls
clus              0  1
  RBMX MUTATED    3  0
  RBMX WILD-TYPE 63  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      3    0
  RBMX WILD-TYPE   63    4
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0            3             63
  1            0              4
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus              0  1
  RBMX MUTATED    2  3
  RBMX WILD-TYPE 65 76
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      2    3
  RBMX WILD-TYPE   65   76
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  FEMALE            2             65
  MALE              3             76
[1] 2 2
[1] FALSE
D23V8, binary
                cls
clus              0  1
  RBMX MUTATED    3  1
  RBMX WILD-TYPE 91 35
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      3    1
  RBMX WILD-TYPE   91   35
     clus
vv    RBMX MUTATED RBMX WILD-TYPE
  NO             3             91
  YES            1             35
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBMX MUTATED                                     3
  RBMX WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBMX MUTATED                                       1
  RBMX WILD-TYPE                                    12
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBMX MUTATED                                                  0
  RBMX WILD-TYPE                                                2
D23V9, multiclass
                                                  clus
vv                                                 RBMX MUTATED RBMX WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             12
  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"
D23V10, continuous
D23V11, continuous
                vv
clus             R0 R1 R2 RX
  RBMX MUTATED    2  2  0  0
  RBMX WILD-TYPE 77 48  4  3
D23V12, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  R0            2             77
  R1            2             48
  R2            0              4
  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"
D23V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBMX MUTATED       0                         0     5
  RBMX WILD-TYPE     9                         5   123
D23V14, multiclass
                           clus
vv                          RBMX MUTATED RBMX WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            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"
D23V15, binary
                cls
clus               0   1
  RBMX MUTATED     0   3
  RBMX WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      0    3
  RBMX WILD-TYPE    5  102
                        clus
vv                       RBMX MUTATED RBMX WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(24) Variable = ESPN MUTATION ANALYSIS
D24V1, survival
                sevent
clus2             0  1
  ESPN MUTATED    4  2
  ESPN WILD-TYPE 64 74
  ESPN MUTATED ESPN WILD-TYPE 
             6            138 
  ESPN MUTATED ESPN WILD-TYPE 
             2             74 
$`ESPN MUTATED`
TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IX TCGA-HV-A5A4 TCGA-IB-AAUR TCGA-YB-A89D 
       20.84        24.26        34.09         7.63        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        42.31        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        58.98        43.50         7.36        33.57        15.06 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        24.43        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       16.37         0.03         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-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
        4.21         9.50        66.94         8.28        30.25        17.49 
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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       16.37        31.27        23.67        12.76        66.28        15.35 

  ESPN MUTATED ESPN WILD-TYPE 
          7.63           0.03 
  ESPN MUTATED ESPN WILD-TYPE 
         34.09          75.12 
  ESPN MUTATED ESPN WILD-TYPE 
        16.175         14.285 
[1] "7.6 - 34.1 (16.2)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.9"
D24V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ESPN MUTATED          1        0         2         3         0        0
  ESPN WILD-TYPE        2        8        21       100         4        4
D24V3, multiclass
           clus
vv          ESPN MUTATED ESPN WILD-TYPE
  STAGE IA             1              2
  STAGE IB             0              8
  STAGE IIA            2             21
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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     5
  ESPN WILD-TYPE   3  16   120
D24V4, multiclass
       clus
vv      ESPN MUTATED ESPN WILD-TYPE
  T1               1              3
  T2               0             16
  T3+T4            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"
D24V5, binary
                cls
clus               0   1
  ESPN MUTATED     3   3
  ESPN WILD-TYPE  34 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESPN MUTATED      3    3
  ESPN WILD-TYPE   34  105
   clus
vv  ESPN MUTATED ESPN WILD-TYPE
  0            3             34
  1            3            105
[1] 2 2
[1] FALSE
D24V6, binary
                cls
clus              0  1
  ESPN MUTATED    1  0
  ESPN WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESPN MUTATED      1    0
  ESPN WILD-TYPE   65    4
   clus
vv  ESPN MUTATED ESPN WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D24V7, binary
                cls
clus              0  1
  ESPN MUTATED    2  4
  ESPN WILD-TYPE 65 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESPN MUTATED      2    4
  ESPN WILD-TYPE   65   75
        clus
vv       ESPN MUTATED ESPN WILD-TYPE
  FEMALE            2             65
  MALE              4             75
[1] 2 2
[1] FALSE
D24V8, binary
                cls
clus              0  1
  ESPN MUTATED    2  4
  ESPN WILD-TYPE 92 32
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESPN MUTATED      2    4
  ESPN WILD-TYPE   92   32
     clus
vv    ESPN MUTATED ESPN WILD-TYPE
  NO             2             92
  YES            4             32
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ESPN MUTATED                                     6
  ESPN WILD-TYPE                                 124
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ESPN MUTATED                                       0
  ESPN WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ESPN MUTATED                                                  0
  ESPN WILD-TYPE                                                2
D24V9, multiclass
                                                  clus
vv                                                 ESPN MUTATED ESPN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6            124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D24V10, continuous
[1] "Remove cluster labels:" "ESPN MUTATED"          
clus
  ESPN MUTATED ESPN WILD-TYPE 
             2             48 
    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-HV-AA8V     TCGA-HZ-A77Q 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644     TCGA-IB-7649 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"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-IB-AAUU     TCGA-LB-A7SX 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
D24V11, continuous
[1] "Remove cluster labels:" "ESPN MUTATED"          
clus
  ESPN MUTATED ESPN WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"ESPN WILD-TYPE" "ESPN WILD-TYPE" "ESPN WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  ESPN MUTATED    4  1  0  0
  ESPN WILD-TYPE 75 49  4  3
D24V12, multiclass
    clus
vv   ESPN MUTATED ESPN WILD-TYPE
  R0            4             75
  R1            1             49
  R2            0              4
  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"
D24V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ESPN MUTATED       1                         0     5
  ESPN WILD-TYPE     8                         5   123
D24V14, multiclass
                           clus
vv                          ESPN MUTATED ESPN WILD-TYPE
  ASIAN                                1              8
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            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"
D24V15, binary
                cls
clus               0   1
  ESPN MUTATED     0   5
  ESPN WILD-TYPE   5 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESPN MUTATED      0    5
  ESPN WILD-TYPE    5  100
                        clus
vv                       ESPN MUTATED ESPN WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5            100
[1] 2 2
[1] FALSE

Clustering(25) Variable = FNDC1 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2              0  1
  FNDC1 MUTATED    4 10
  FNDC1 WILD-TYPE 64 66
  FNDC1 MUTATED FNDC1 WILD-TYPE 
             14             130 
  FNDC1 MUTATED FNDC1 WILD-TYPE 
             10              66 
$`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        19.59        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-XN-A8T3 TCGA-YB-A89D 
       31.27        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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX 
       43.50        20.84        24.26        33.57        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        24.43        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        19.50         0.13        20.19        17.03        23.21 
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-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       15.81        19.66        21.30         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-AAUR 
        8.22        15.88         0.26         4.73         7.86        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        24.23        17.26        22.85        39.98        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        16.37 
TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        12.76        66.28        15.35 

  FNDC1 MUTATED FNDC1 WILD-TYPE 
           3.85            0.03 
  FNDC1 MUTATED FNDC1 WILD-TYPE 
          31.27           75.12 
  FNDC1 MUTATED FNDC1 WILD-TYPE 
         15.075          14.270 
[1] "3.9 - 31.3 (15.1)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.4"
D25V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FNDC1 MUTATED          0        1         1        11         1        0
  FNDC1 WILD-TYPE        3        7        22        92         3        4
D25V3, multiclass
           clus
vv          FNDC1 MUTATED FNDC1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             1              22
  STAGE IIB            11              92
  STAGE III             1               3
  STAGE IV              0               4
[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   2    12
  FNDC1 WILD-TYPE   4  14   113
D25V4, multiclass
       clus
vv      FNDC1 MUTATED FNDC1 WILD-TYPE
  T1                0               4
  T2                2              14
  T3+T4            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"
D25V5, binary
                 cls
clus               0  1
  FNDC1 MUTATED    3 11
  FNDC1 WILD-TYPE 34 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC1 MUTATED      3   11
  FNDC1 WILD-TYPE   34   97
   clus
vv  FNDC1 MUTATED FNDC1 WILD-TYPE
  0             3              34
  1            11              97
[1] 2 2
[1] FALSE
D25V6, binary
                 cls
clus               0  1
  FNDC1 MUTATED    7  0
  FNDC1 WILD-TYPE 59  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC1 MUTATED      7    0
  FNDC1 WILD-TYPE   59    4
   clus
vv  FNDC1 MUTATED FNDC1 WILD-TYPE
  0             7              59
  1             0               4
[1] 2 2
[1] FALSE
D25V7, binary
                 cls
clus               0  1
  FNDC1 MUTATED    7  7
  FNDC1 WILD-TYPE 60 72
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC1 MUTATED      7    7
  FNDC1 WILD-TYPE   60   72
        clus
vv       FNDC1 MUTATED FNDC1 WILD-TYPE
  FEMALE             7              60
  MALE               7              72
[1] 2 2
[1] FALSE
D25V8, binary
                 cls
clus               0  1
  FNDC1 MUTATED   10  4
  FNDC1 WILD-TYPE 84 32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC1 MUTATED     10    4
  FNDC1 WILD-TYPE   84   32
     clus
vv    FNDC1 MUTATED FNDC1 WILD-TYPE
  NO             10              84
  YES             4              32
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FNDC1 MUTATED                                    14
  FNDC1 WILD-TYPE                                 116
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FNDC1 MUTATED                                       0
  FNDC1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FNDC1 MUTATED                                                  0
  FNDC1 WILD-TYPE                                                2
D25V9, multiclass
                                                  clus
vv                                                 FNDC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         14
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 FNDC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          116
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D25V10, continuous
D25V11, continuous
                 vv
clus              R0 R1 R2 RX
  FNDC1 MUTATED    9  5  0  0
  FNDC1 WILD-TYPE 70 45  4  3
D25V12, multiclass
    clus
vv   FNDC1 MUTATED FNDC1 WILD-TYPE
  R0             9              70
  R1             5              45
  R2             0               4
  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"
D25V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FNDC1 MUTATED       0                         0    14
  FNDC1 WILD-TYPE     9                         5   114
D25V14, multiclass
                           clus
vv                          FNDC1 MUTATED FNDC1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                14             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"
D25V15, binary
                 cls
clus               0  1
  FNDC1 MUTATED    1 10
  FNDC1 WILD-TYPE  4 95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC1 MUTATED      1   10
  FNDC1 WILD-TYPE    4   95
                        clus
vv                       FNDC1 MUTATED FNDC1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO            10              95
[1] 2 2
[1] FALSE

Clustering(26) Variable = ATP2C1 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2               0  1
  ATP2C1 MUTATED    1  7
  ATP2C1 WILD-TYPE 67 69
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               8              136 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
               7               69 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 TCGA-HZ-8002 
       30.25        17.49        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 
       19.59         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-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 
       10.85         1.08         0.23        19.82        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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G 
       17.26        23.08        22.85        39.98        16.80         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
           10.98             0.03 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
           20.19            75.12 
  ATP2C1 MUTATED ATP2C1 WILD-TYPE 
          15.630           14.005 
[1] "11.0 - 20.2 (15.6)" "0.0 - 75.1 (14.0)" 
[1] "hr=" "1.8"
D26V2, 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        3        8        23        96         4        3
D26V3, multiclass
           clus
vv          ATP2C1 MUTATED ATP2C1 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              7               96
  STAGE III              0                4
  STAGE IV               1                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
  ATP2C1 MUTATED     0   0     8
  ATP2C1 WILD-TYPE   4  16   117
D26V4, multiclass
       clus
vv      ATP2C1 MUTATED ATP2C1 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D26V5, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED     0   8
  ATP2C1 WILD-TYPE  37 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      0    8
  ATP2C1 WILD-TYPE   37  100
   clus
vv  ATP2C1 MUTATED ATP2C1 WILD-TYPE
  0              0               37
  1              8              100
[1] 2 2
[1] FALSE
D26V6, binary
                  cls
clus                0  1
  ATP2C1 MUTATED    4  1
  ATP2C1 WILD-TYPE 62  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      4    1
  ATP2C1 WILD-TYPE   62    3
   clus
vv  ATP2C1 MUTATED ATP2C1 WILD-TYPE
  0              4               62
  1              1                3
[1] 2 2
[1] FALSE
D26V7, binary
                  cls
clus                0  1
  ATP2C1 MUTATED    3  5
  ATP2C1 WILD-TYPE 64 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      3    5
  ATP2C1 WILD-TYPE   64   74
        clus
vv       ATP2C1 MUTATED ATP2C1 WILD-TYPE
  FEMALE              3               64
  MALE                5               74
[1] 2 2
[1] FALSE
D26V8, binary
                  cls
clus                0  1
  ATP2C1 MUTATED    6  1
  ATP2C1 WILD-TYPE 88 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      6    1
  ATP2C1 WILD-TYPE   88   35
     clus
vv    ATP2C1 MUTATED ATP2C1 WILD-TYPE
  NO               6               88
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP2C1 MUTATED                                     6
  ATP2C1 WILD-TYPE                                 124
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP2C1 MUTATED                                       2
  ATP2C1 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP2C1 MUTATED                                                  0
  ATP2C1 WILD-TYPE                                                2
D26V9, 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                           124
  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"
D26V10, continuous
D26V11, continuous
                  vv
clus               R0 R1 R2 RX
  ATP2C1 MUTATED    3  4  0  1
  ATP2C1 WILD-TYPE 76 46  4  2
D26V12, multiclass
    clus
vv   ATP2C1 MUTATED ATP2C1 WILD-TYPE
  R0              3               76
  R1              4               46
  R2              0                4
  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"
D26V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP2C1 MUTATED       0                         1     6
  ATP2C1 WILD-TYPE     9                         4   122
D26V14, multiclass
                           clus
vv                          ATP2C1 MUTATED ATP2C1 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  6              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"
D26V15, binary
                  cls
clus                 0   1
  ATP2C1 MUTATED     0   5
  ATP2C1 WILD-TYPE   5 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C1 MUTATED      0    5
  ATP2C1 WILD-TYPE    5  100
                        clus
vv                       ATP2C1 MUTATED ATP2C1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5              100
[1] 2 2
[1] FALSE

Clustering(27) Variable = HACL1 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2              0  1
  HACL1 MUTATED    0  5
  HACL1 WILD-TYPE 68 71
  HACL1 MUTATED HACL1 WILD-TYPE 
              5             139 
  HACL1 MUTATED HACL1 WILD-TYPE 
              5              71 
$`HACL1 MUTATED`
TCGA-HV-A5A3 TCGA-HZ-7919 TCGA-HZ-8003 TCGA-IB-7645 TCGA-S4-A8RP 
        4.21        19.50        19.59        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
        1.02        12.89        13.84         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
        8.28        30.25        17.49         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        12.95 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-US-A774 TCGA-US-A776 
       15.32         9.40        24.23        17.26        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HACL1 MUTATED HACL1 WILD-TYPE 
           4.21            0.03 
  HACL1 MUTATED HACL1 WILD-TYPE 
          49.38           75.12 
  HACL1 MUTATED HACL1 WILD-TYPE 
          19.59           14.14 
[1] "4.2 - 49.4 (19.6)" "0.0 - 75.1 (14.1)"
[1] "hr=" "1.3"
D27V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  HACL1 MUTATED          0        0         1         4         0        0
  HACL1 WILD-TYPE        3        8        22        99         4        4
D27V3, multiclass
           clus
vv          HACL1 MUTATED HACL1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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     5
  HACL1 WILD-TYPE   4  16   120
D27V4, multiclass
       clus
vv      HACL1 MUTATED HACL1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D27V5, binary
                 cls
clus                0   1
  HACL1 MUTATED     0   4
  HACL1 WILD-TYPE  37 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HACL1 MUTATED      0    4
  HACL1 WILD-TYPE   37  104
   clus
vv  HACL1 MUTATED HACL1 WILD-TYPE
  0             0              37
  1             4             104
[1] 2 2
[1] FALSE
D27V6, binary
                 cls
clus               0  1
  HACL1 MUTATED    2  0
  HACL1 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HACL1 MUTATED      2    0
  HACL1 WILD-TYPE   64    4
   clus
vv  HACL1 MUTATED HACL1 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D27V7, binary
                 cls
clus               0  1
  HACL1 MUTATED    4  1
  HACL1 WILD-TYPE 63 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HACL1 MUTATED      4    1
  HACL1 WILD-TYPE   63   78
        clus
vv       HACL1 MUTATED HACL1 WILD-TYPE
  FEMALE             4              63
  MALE               1              78
[1] 2 2
[1] FALSE
D27V8, binary
                 cls
clus               0  1
  HACL1 MUTATED    3  1
  HACL1 WILD-TYPE 91 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HACL1 MUTATED      3    1
  HACL1 WILD-TYPE   91   35
     clus
vv    HACL1 MUTATED HACL1 WILD-TYPE
  NO              3              91
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HACL1 MUTATED                                     5
  HACL1 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HACL1 MUTATED                                       0
  HACL1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HACL1 MUTATED                                                  0
  HACL1 WILD-TYPE                                                2
D27V9, multiclass
                                                  clus
vv                                                 HACL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 HACL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D27V10, continuous
[1] "Remove cluster labels:" "HACL1 MUTATED"         
clus
  HACL1 MUTATED HACL1 WILD-TYPE 
              1              49 
     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-HV-AA8V      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" "HACL1 WILD-TYPE" 
     TCGA-YY-A8LH 
"HACL1 WILD-TYPE" 
D27V11, continuous
                 vv
clus              R0 R1 R2 RX
  HACL1 MUTATED    3  1  0  0
  HACL1 WILD-TYPE 76 49  4  3
D27V12, multiclass
    clus
vv   HACL1 MUTATED HACL1 WILD-TYPE
  R0             3              76
  R1             1              49
  R2             0               4
  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"
D27V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HACL1 MUTATED       1                         0     3
  HACL1 WILD-TYPE     8                         5   125
D27V14, multiclass
                           clus
vv                          HACL1 MUTATED HACL1 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
                 cls
clus                0   1
  HACL1 MUTATED     0   2
  HACL1 WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HACL1 MUTATED      0    2
  HACL1 WILD-TYPE    5  103
                        clus
vv                       HACL1 MUTATED HACL1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(28) Variable = UBAC1 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2              0  1
  UBAC1 MUTATED    2  3
  UBAC1 WILD-TYPE 66 73
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              5             139 
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7925 
       66.94         8.28        30.25        17.49        19.50        20.19 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       41.33         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-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 
       10.29         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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  UBAC1 MUTATED UBAC1 WILD-TYPE 
           0.13            0.03 
  UBAC1 MUTATED UBAC1 WILD-TYPE 
          19.20           75.12 
  UBAC1 MUTATED UBAC1 WILD-TYPE 
           4.04           14.40 
[1] "0.1 - 19.2 (4.0)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "2.3"
D28V2, 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        3        8        22        99         4        4
D28V3, multiclass
           clus
vv          UBAC1 MUTATED UBAC1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   120
D28V4, multiclass
       clus
vv      UBAC1 MUTATED UBAC1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D28V5, binary
                 cls
clus                0   1
  UBAC1 MUTATED     1   4
  UBAC1 WILD-TYPE  36 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAC1 MUTATED      1    4
  UBAC1 WILD-TYPE   36  104
   clus
vv  UBAC1 MUTATED UBAC1 WILD-TYPE
  0             1              36
  1             4             104
[1] 2 2
[1] FALSE
D28V6, binary
                 cls
clus               0  1
  UBAC1 MUTATED    2  0
  UBAC1 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAC1 MUTATED      2    0
  UBAC1 WILD-TYPE   64    4
   clus
vv  UBAC1 MUTATED UBAC1 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D28V7, binary
                 cls
clus               0  1
  UBAC1 MUTATED    2  3
  UBAC1 WILD-TYPE 65 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAC1 MUTATED      2    3
  UBAC1 WILD-TYPE   65   76
        clus
vv       UBAC1 MUTATED UBAC1 WILD-TYPE
  FEMALE             2              65
  MALE               3              76
[1] 2 2
[1] FALSE
D28V8, binary
                 cls
clus               0  1
  UBAC1 MUTATED    2  1
  UBAC1 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAC1 MUTATED      2    1
  UBAC1 WILD-TYPE   92   35
     clus
vv    UBAC1 MUTATED UBAC1 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UBAC1 MUTATED                                     5
  UBAC1 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UBAC1 MUTATED                                       0
  UBAC1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UBAC1 MUTATED                                                  0
  UBAC1 WILD-TYPE                                                2
D28V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D28V10, continuous
[1] "Remove cluster labels:" "UBAC1 MUTATED"         
clus
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
     TCGA-YY-A8LH 
"UBAC1 WILD-TYPE" 
D28V11, continuous
[1] "Remove cluster labels:" "UBAC1 MUTATED"         
clus
  UBAC1 MUTATED UBAC1 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" "UBAC1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  UBAC1 MUTATED    1  3  0  1
  UBAC1 WILD-TYPE 78 47  4  2
D28V12, multiclass
    clus
vv   UBAC1 MUTATED UBAC1 WILD-TYPE
  R0             1              78
  R1             3              47
  R2             0               4
  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"
D28V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBAC1 MUTATED       0                         1     3
  UBAC1 WILD-TYPE     9                         4   125
D28V14, multiclass
                           clus
vv                          UBAC1 MUTATED UBAC1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                 cls
clus                0   1
  UBAC1 MUTATED     0   4
  UBAC1 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBAC1 MUTATED      0    4
  UBAC1 WILD-TYPE    5  101
                        clus
vv                       UBAC1 MUTATED UBAC1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(29) Variable = OGFOD1 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2               0  1
  OGFOD1 MUTATED    3  2
  OGFOD1 WILD-TYPE 65 74
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               5              139 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               2               74 
$`OGFOD1 MUTATED`
TCGA-H6-8124 TCGA-HV-AA8X TCGA-HZ-8519 TCGA-IB-7888 TCGA-IB-8126 
       12.89        17.49        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
        1.02        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
        8.28        30.25        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-7889 TCGA-IB-7890 TCGA-IB-7891 
       41.33         4.04         3.62        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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
            2.47             0.03 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
           43.79            75.12 
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
           14.93            14.17 
[1] "2.5 - 43.8 (14.9)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.4"
D29V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OGFOD1 MUTATED          1        0         1         2         1        0
  OGFOD1 WILD-TYPE        2        8        22       101         3        4
D29V3, multiclass
           clus
vv          OGFOD1 MUTATED OGFOD1 WILD-TYPE
  STAGE IA               1                2
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              2              101
  STAGE III              1                3
  STAGE IV               0                4
[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   1     3
  OGFOD1 WILD-TYPE   3  15   122
D29V4, multiclass
       clus
vv      OGFOD1 MUTATED OGFOD1 WILD-TYPE
  T1                 1                3
  T2                 1               15
  T3+T4              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"
D29V5, binary
                  cls
clus                 0   1
  OGFOD1 MUTATED     2   3
  OGFOD1 WILD-TYPE  35 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      2    3
  OGFOD1 WILD-TYPE   35  105
   clus
vv  OGFOD1 MUTATED OGFOD1 WILD-TYPE
  0              2               35
  1              3              105
[1] 2 2
[1] FALSE
D29V6, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    3  0
  OGFOD1 WILD-TYPE 63  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      3    0
  OGFOD1 WILD-TYPE   63    4
   clus
vv  OGFOD1 MUTATED OGFOD1 WILD-TYPE
  0              3               63
  1              0                4
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    4  1
  OGFOD1 WILD-TYPE 63 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      4    1
  OGFOD1 WILD-TYPE   63   78
        clus
vv       OGFOD1 MUTATED OGFOD1 WILD-TYPE
  FEMALE              4               63
  MALE                1               78
[1] 2 2
[1] FALSE
D29V8, binary
                  cls
clus                0  1
  OGFOD1 MUTATED    2  2
  OGFOD1 WILD-TYPE 92 34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      2    2
  OGFOD1 WILD-TYPE   92   34
     clus
vv    OGFOD1 MUTATED OGFOD1 WILD-TYPE
  NO               2               92
  YES              2               34
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OGFOD1 MUTATED                                     4
  OGFOD1 WILD-TYPE                                 126
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OGFOD1 MUTATED                                       1
  OGFOD1 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OGFOD1 MUTATED                                                  0
  OGFOD1 WILD-TYPE                                                2
D29V9, multiclass
                                                  clus
vv                                                 OGFOD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 OGFOD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D29V10, continuous
[1] "Remove cluster labels:" "OGFOD1 MUTATED"        
clus
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               2               48 
      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-HV-AA8V 
"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-7887       TCGA-IB-7891       TCGA-IB-8127       TCGA-IB-A5SS 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
D29V11, continuous
[1] "Remove cluster labels:" "OGFOD1 MUTATED"        
clus
  OGFOD1 MUTATED OGFOD1 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"OGFOD1 WILD-TYPE" "OGFOD1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  OGFOD1 MUTATED    3  1  1  0
  OGFOD1 WILD-TYPE 76 49  3  3
D29V12, multiclass
    clus
vv   OGFOD1 MUTATED OGFOD1 WILD-TYPE
  R0              3               76
  R1              1               49
  R2              1                3
  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"
D29V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OGFOD1 MUTATED       1                         1     3
  OGFOD1 WILD-TYPE     8                         4   125
D29V14, multiclass
                           clus
vv                          OGFOD1 MUTATED OGFOD1 WILD-TYPE
  ASIAN                                  1                8
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, binary
                  cls
clus                 0   1
  OGFOD1 MUTATED     0   4
  OGFOD1 WILD-TYPE   5 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFOD1 MUTATED      0    4
  OGFOD1 WILD-TYPE    5  101
                        clus
vv                       OGFOD1 MUTATED OGFOD1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              101
[1] 2 2
[1] FALSE

Clustering(30) Variable = CASQ2 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2              0  1
  CASQ2 MUTATED    6  2
  CASQ2 WILD-TYPE 62 74
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              8             136 
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              2              74 
$`CASQ2 MUTATED`
TCGA-H6-8124 TCGA-HV-A5A5 TCGA-HZ-A4BH TCGA-HZ-A77Q TCGA-IB-7647 TCGA-IB-7887 
       12.89         9.50         6.38         1.08        21.90         3.62 
TCGA-LB-A8F3 TCGA-US-A776 
       12.46        39.98 

$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 TCGA-HV-A7OL 
        1.02        13.84         4.21         7.63        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         0.23        19.82        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
        4.77        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-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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       17.26        23.08        22.85        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  CASQ2 MUTATED CASQ2 WILD-TYPE 
           1.08            0.03 
  CASQ2 MUTATED CASQ2 WILD-TYPE 
          39.98           75.12 
  CASQ2 MUTATED CASQ2 WILD-TYPE 
          10.98           14.70 
[1] "1.1 - 40.0 (11.0)" "0.0 - 75.1 (14.7)"
[1] "hr=" "1.6"
D30V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CASQ2 MUTATED          0        0         2         6         0        0
  CASQ2 WILD-TYPE        3        8        21        97         4        4
D30V3, multiclass
           clus
vv          CASQ2 MUTATED CASQ2 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             2              21
  STAGE IIB             6              97
  STAGE III             0               4
  STAGE IV              0               4
[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     8
  CASQ2 WILD-TYPE   4  16   117
D30V4, multiclass
       clus
vv      CASQ2 MUTATED CASQ2 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D30V5, binary
                 cls
clus                0   1
  CASQ2 MUTATED     2   6
  CASQ2 WILD-TYPE  35 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASQ2 MUTATED      2    6
  CASQ2 WILD-TYPE   35  102
   clus
vv  CASQ2 MUTATED CASQ2 WILD-TYPE
  0             2              35
  1             6             102
[1] 2 2
[1] FALSE
D30V6, binary
                 cls
clus               0  1
  CASQ2 MUTATED    4  0
  CASQ2 WILD-TYPE 62  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASQ2 MUTATED      4    0
  CASQ2 WILD-TYPE   62    4
   clus
vv  CASQ2 MUTATED CASQ2 WILD-TYPE
  0             4              62
  1             0               4
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus               0  1
  CASQ2 MUTATED    5  3
  CASQ2 WILD-TYPE 62 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASQ2 MUTATED      5    3
  CASQ2 WILD-TYPE   62   76
        clus
vv       CASQ2 MUTATED CASQ2 WILD-TYPE
  FEMALE             5              62
  MALE               3              76
[1] 2 2
[1] FALSE
D30V8, binary
                 cls
clus               0  1
  CASQ2 MUTATED    4  2
  CASQ2 WILD-TYPE 90 34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASQ2 MUTATED      4    2
  CASQ2 WILD-TYPE   90   34
     clus
vv    CASQ2 MUTATED CASQ2 WILD-TYPE
  NO              4              90
  YES             2              34
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CASQ2 MUTATED                                     6
  CASQ2 WILD-TYPE                                 124
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CASQ2 MUTATED                                       1
  CASQ2 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CASQ2 MUTATED                                                  1
  CASQ2 WILD-TYPE                                                1
D30V9, multiclass
                                                  clus
vv                                                 CASQ2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 CASQ2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D30V10, continuous
D30V11, continuous
[1] "Remove cluster labels:" "CASQ2 MUTATED"         
clus
  CASQ2 MUTATED CASQ2 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"CASQ2 WILD-TYPE" "CASQ2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CASQ2 MUTATED    4  3  0  0
  CASQ2 WILD-TYPE 75 47  4  3
D30V12, multiclass
    clus
vv   CASQ2 MUTATED CASQ2 WILD-TYPE
  R0             4              75
  R1             3              47
  R2             0               4
  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"
D30V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CASQ2 MUTATED       1                         1     6
  CASQ2 WILD-TYPE     8                         4   122
D30V14, multiclass
                           clus
vv                          CASQ2 MUTATED CASQ2 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 6             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"
D30V15, binary
                 cls
clus               0  1
  CASQ2 MUTATED    0  6
  CASQ2 WILD-TYPE  5 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASQ2 MUTATED      0    6
  CASQ2 WILD-TYPE    5   99
                        clus
vv                       CASQ2 MUTATED CASQ2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              99
[1] 2 2
[1] FALSE

Clustering(31) Variable = TGFBR2 MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2               0  1
  TGFBR2 MUTATED    2  6
  TGFBR2 WILD-TYPE 66 70
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               8              136 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               6               70 
$`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        15.35 

$`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        42.31        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        58.98        43.50 
TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
       20.84         7.36        33.57        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       24.43        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        12.66        16.37 
TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
        0.03         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-HV-A5A3 
        4.04         5.03         1.02        12.89        13.84         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
        7.63         9.50        66.94         8.28        30.25        17.49 
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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
        0.39        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       23.67        11.51        12.76        66.28 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            2.17             0.03 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
           41.33            75.12 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          14.150           14.285 
[1] "2.2 - 41.3 (14.1)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.4"
D31V2, 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        3        8        22        97         3        4
D31V3, multiclass
           clus
vv          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              6               97
  STAGE III              1                3
  STAGE IV               0                4
[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   4  16   117
D31V4, multiclass
       clus
vv      TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D31V5, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     2   6
  TGFBR2 WILD-TYPE  35 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      2    6
  TGFBR2 WILD-TYPE   35  102
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0              2               35
  1              6              102
[1] 2 2
[1] FALSE
D31V6, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    5  0
  TGFBR2 WILD-TYPE 61  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      5    0
  TGFBR2 WILD-TYPE   61    4
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0              5               61
  1              0                4
[1] 2 2
[1] FALSE
D31V7, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    5  3
  TGFBR2 WILD-TYPE 62 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      5    3
  TGFBR2 WILD-TYPE   62   76
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              5               62
  MALE                3               76
[1] 2 2
[1] FALSE
D31V8, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    7  1
  TGFBR2 WILD-TYPE 87 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      7    1
  TGFBR2 WILD-TYPE   87   35
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO               7               87
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGFBR2 MUTATED                                     7
  TGFBR2 WILD-TYPE                                 123
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGFBR2 MUTATED                                       1
  TGFBR2 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGFBR2 MUTATED                                                  0
  TGFBR2 WILD-TYPE                                                2
D31V9, 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                           123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D31V10, continuous
D31V11, continuous
                  vv
clus               R0 R1 R2 RX
  TGFBR2 MUTATED    6  1  0  1
  TGFBR2 WILD-TYPE 73 49  4  2
D31V12, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  R0              6               73
  R1              1               49
  R2              0                4
  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"
D31V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED       0                         0     8
  TGFBR2 WILD-TYPE     9                         5   120
D31V14, multiclass
                           clus
vv                          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              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"
D31V15, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED     0   4
  TGFBR2 WILD-TYPE   5 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0    4
  TGFBR2 WILD-TYPE    5  101
                        clus
vv                       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              101
[1] 2 2
[1] FALSE

Clustering(32) Variable = RNF43 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2              0  1
  RNF43 MUTATED    7  2
  RNF43 WILD-TYPE 61 74
  RNF43 MUTATED RNF43 WILD-TYPE 
              9             135 
  RNF43 MUTATED RNF43 WILD-TYPE 
              2              74 
$`RNF43 MUTATED`
TCGA-2J-AABE TCGA-3E-AAAZ TCGA-HV-A7OL TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-IB-7651 
       22.22        71.74         8.28         1.08         0.23        19.82 
TCGA-IB-8127 TCGA-S4-A8RM TCGA-YY-A8LH 
       17.16        24.23        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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-AA8V 
       13.84         4.21         7.63         9.50        66.94        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
        5.26        10.85        19.82        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        39.98        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       11.51        12.76        15.35 

  RNF43 MUTATED RNF43 WILD-TYPE 
           0.23            0.03 
  RNF43 MUTATED RNF43 WILD-TYPE 
          71.74           75.12 
  RNF43 MUTATED RNF43 WILD-TYPE 
          19.82           14.14 
[1] "0.2 - 71.7 (19.8)" "0.0 - 75.1 (14.1)"
[1] "hr=" "4.1"
D32V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RNF43 MUTATED          0        1         3         5         0        0
  RNF43 WILD-TYPE        3        7        20        98         4        4
D32V3, multiclass
           clus
vv          RNF43 MUTATED RNF43 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             3              20
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              0               4
[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   1     8
  RNF43 WILD-TYPE   4  15   117
D32V4, multiclass
       clus
vv      RNF43 MUTATED RNF43 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D32V5, binary
                 cls
clus                0   1
  RNF43 MUTATED     4   5
  RNF43 WILD-TYPE  33 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      4    5
  RNF43 WILD-TYPE   33  103
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0             4              33
  1             5             103
[1] 2 2
[1] FALSE
D32V6, binary
                 cls
clus               0  1
  RNF43 MUTATED    3  0
  RNF43 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      3    0
  RNF43 WILD-TYPE   63    4
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D32V7, binary
                 cls
clus               0  1
  RNF43 MUTATED    3  6
  RNF43 WILD-TYPE 64 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      3    6
  RNF43 WILD-TYPE   64   73
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  FEMALE             3              64
  MALE               6              73
[1] 2 2
[1] FALSE
D32V8, binary
                 cls
clus               0  1
  RNF43 MUTATED    4  2
  RNF43 WILD-TYPE 90 34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      4    2
  RNF43 WILD-TYPE   90   34
     clus
vv    RNF43 MUTATED RNF43 WILD-TYPE
  NO              4              90
  YES             2              34
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RNF43 MUTATED                                     8
  RNF43 WILD-TYPE                                 122
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RNF43 MUTATED                                       1
  RNF43 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RNF43 MUTATED                                                  0
  RNF43 WILD-TYPE                                                2
D32V9, multiclass
                                                  clus
vv                                                 RNF43 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RNF43 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          122
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D32V10, continuous
D32V11, continuous
                 vv
clus              R0 R1 R2 RX
  RNF43 MUTATED    6  1  1  0
  RNF43 WILD-TYPE 73 49  3  3
D32V12, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  R0             6              73
  R1             1              49
  R2             1               3
  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"
D32V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF43 MUTATED       1                         0     8
  RNF43 WILD-TYPE     8                         5   120
D32V14, multiclass
                           clus
vv                          RNF43 MUTATED RNF43 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 8             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"
D32V15, binary
                 cls
clus               0  1
  RNF43 MUTATED    1  6
  RNF43 WILD-TYPE  4 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED      1    6
  RNF43 WILD-TYPE    4   99
                        clus
vv                       RNF43 MUTATED RNF43 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             6              99
[1] 2 2
[1] FALSE

Clustering(33) Variable = DCP1B MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2              0  1
  DCP1B MUTATED    4  4
  DCP1B WILD-TYPE 64 72
  DCP1B MUTATED DCP1B WILD-TYPE 
              8             136 
  DCP1B MUTATED DCP1B WILD-TYPE 
              4              72 
$`DCP1B MUTATED`
TCGA-HV-A5A4 TCGA-HZ-8003 TCGA-HZ-A49H TCGA-IB-7651 TCGA-IB-7652 TCGA-LB-A7SX 
        7.63        19.59        16.14        19.82        23.80        12.92 
TCGA-US-A77G TCGA-XN-A8T3 
        0.39        31.27 

$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A5A6 
        1.02        12.89        13.84         4.21         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-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 
       24.23        17.26        23.08        22.85        39.98        16.80 
TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 
       14.14        13.81        12.99        12.03        16.37        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  DCP1B MUTATED DCP1B WILD-TYPE 
           0.39            0.03 
  DCP1B MUTATED DCP1B WILD-TYPE 
          31.27           75.12 
  DCP1B MUTATED DCP1B WILD-TYPE 
         17.865          14.155 
[1] "0.4 - 31.3 (17.9)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.2"
D33V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DCP1B MUTATED          0        1         1         7         0        0
  DCP1B WILD-TYPE        3        7        22        96         4        4
D33V3, multiclass
           clus
vv          DCP1B MUTATED DCP1B WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             1              22
  STAGE IIB             7              96
  STAGE III             0               4
  STAGE IV              0               4
[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   1     8
  DCP1B WILD-TYPE   4  15   117
D33V4, multiclass
       clus
vv      DCP1B MUTATED DCP1B WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D33V5, binary
                 cls
clus                0   1
  DCP1B MUTATED     2   7
  DCP1B WILD-TYPE  35 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCP1B MUTATED      2    7
  DCP1B WILD-TYPE   35  101
   clus
vv  DCP1B MUTATED DCP1B WILD-TYPE
  0             2              35
  1             7             101
[1] 2 2
[1] FALSE
D33V6, binary
                 cls
clus               0  1
  DCP1B MUTATED    3  0
  DCP1B WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCP1B MUTATED      3    0
  DCP1B WILD-TYPE   63    4
   clus
vv  DCP1B MUTATED DCP1B WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus               0  1
  DCP1B MUTATED    7  2
  DCP1B WILD-TYPE 60 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCP1B MUTATED      7    2
  DCP1B WILD-TYPE   60   77
        clus
vv       DCP1B MUTATED DCP1B WILD-TYPE
  FEMALE             7              60
  MALE               2              77
[1] 2 2
[1] FALSE
D33V8, binary
                 cls
clus               0  1
  DCP1B MUTATED    7  1
  DCP1B WILD-TYPE 87 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCP1B MUTATED      7    1
  DCP1B WILD-TYPE   87   35
     clus
vv    DCP1B MUTATED DCP1B WILD-TYPE
  NO              7              87
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DCP1B MUTATED                                     9
  DCP1B WILD-TYPE                                 121
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DCP1B MUTATED                                       0
  DCP1B WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DCP1B MUTATED                                                  0
  DCP1B WILD-TYPE                                                2
D33V9, multiclass
                                                  clus
vv                                                 DCP1B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 DCP1B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          121
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D33V10, continuous
[1] "Remove cluster labels:" "DCP1B MUTATED"         
clus
  DCP1B MUTATED DCP1B WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
D33V11, continuous
[1] "Remove cluster labels:" "DCP1B MUTATED"         
clus
  DCP1B MUTATED DCP1B WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"DCP1B WILD-TYPE" "DCP1B WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  DCP1B MUTATED    5  3  0  0
  DCP1B WILD-TYPE 74 47  4  3
D33V12, multiclass
    clus
vv   DCP1B MUTATED DCP1B WILD-TYPE
  R0             5              74
  R1             3              47
  R2             0               4
  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"
D33V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DCP1B MUTATED       2                         1     6
  DCP1B WILD-TYPE     7                         4   122
D33V14, multiclass
                           clus
vv                          DCP1B MUTATED DCP1B WILD-TYPE
  ASIAN                                 2               7
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 6             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"
D33V15, binary
                 cls
clus               0  1
  DCP1B MUTATED    2  6
  DCP1B WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCP1B MUTATED      2    6
  DCP1B WILD-TYPE    3   99
                        clus
vv                       DCP1B MUTATED DCP1B WILD-TYPE
  HISPANIC OR LATINO                 2               3
  NOT HISPANIC OR LATINO             6              99
[1] 2 2
[1] FALSE

Clustering(34) Variable = ZNF678 MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2               0  1
  ZNF678 MUTATED    0  5
  ZNF678 WILD-TYPE 68 71
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               5              139 
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               5               71 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       17.03        23.21        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZNF678 MUTATED ZNF678 WILD-TYPE 
            3.95             0.03 
  ZNF678 MUTATED ZNF678 WILD-TYPE 
           20.19            75.12 
  ZNF678 MUTATED ZNF678 WILD-TYPE 
           15.35            14.17 
[1] "4.0 - 20.2 (15.3)" "0.0 - 75.1 (14.2)"
[1] "hr=" "2.2"
D34V2, 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        3        8        23        98         4        4
D34V3, multiclass
           clus
vv          ZNF678 MUTATED ZNF678 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              5               98
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   120
D34V4, multiclass
       clus
vv      ZNF678 MUTATED ZNF678 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D34V5, binary
                  cls
clus                 0   1
  ZNF678 MUTATED     0   5
  ZNF678 WILD-TYPE  37 103
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF678 MUTATED      0    5
  ZNF678 WILD-TYPE   37  103
   clus
vv  ZNF678 MUTATED ZNF678 WILD-TYPE
  0              0               37
  1              5              103
[1] 2 2
[1] FALSE
D34V6, binary
                  cls
clus                0  1
  ZNF678 MUTATED    2  0
  ZNF678 WILD-TYPE 64  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF678 MUTATED      2    0
  ZNF678 WILD-TYPE   64    4
   clus
vv  ZNF678 MUTATED ZNF678 WILD-TYPE
  0              2               64
  1              0                4
[1] 2 2
[1] FALSE
D34V7, binary
                  cls
clus                0  1
  ZNF678 MUTATED    2  3
  ZNF678 WILD-TYPE 65 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF678 MUTATED      2    3
  ZNF678 WILD-TYPE   65   76
        clus
vv       ZNF678 MUTATED ZNF678 WILD-TYPE
  FEMALE              2               65
  MALE                3               76
[1] 2 2
[1] FALSE
D34V8, binary
                  cls
clus                0  1
  ZNF678 MUTATED    5  0
  ZNF678 WILD-TYPE 89 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF678 MUTATED      5    0
  ZNF678 WILD-TYPE   89   36
     clus
vv    ZNF678 MUTATED ZNF678 WILD-TYPE
  NO               5               89
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF678 MUTATED                                     5
  ZNF678 WILD-TYPE                                 125
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF678 MUTATED                                       0
  ZNF678 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF678 MUTATED                                                  0
  ZNF678 WILD-TYPE                                                2
D34V9, 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                           125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D34V10, continuous
[1] "Remove cluster labels:" "ZNF678 MUTATED"        
clus
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               2               48 
      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-HV-AA8V       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-7887 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
D34V11, continuous
[1] "Remove cluster labels:" "ZNF678 MUTATED"        
clus
  ZNF678 MUTATED ZNF678 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"ZNF678 WILD-TYPE" "ZNF678 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF678 MUTATED    3  2  0  0
  ZNF678 WILD-TYPE 76 48  4  3
D34V12, multiclass
    clus
vv   ZNF678 MUTATED ZNF678 WILD-TYPE
  R0              3               76
  R1              2               48
  R2              0                4
  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"
D34V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF678 MUTATED       0                         0     4
  ZNF678 WILD-TYPE     9                         5   124
D34V14, multiclass
                           clus
vv                          ZNF678 MUTATED ZNF678 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, binary
                  cls
clus                 0   1
  ZNF678 MUTATED     0   4
  ZNF678 WILD-TYPE   5 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF678 MUTATED      0    4
  ZNF678 WILD-TYPE    5  101
                        clus
vv                       ZNF678 MUTATED ZNF678 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              101
[1] 2 2
[1] FALSE

Clustering(35) Variable = RPL22 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2              0  1
  RPL22 MUTATED    2  3
  RPL22 WILD-TYPE 66 73
  RPL22 MUTATED RPL22 WILD-TYPE 
              5             139 
  RPL22 MUTATED RPL22 WILD-TYPE 
              3              73 
$`RPL22 MUTATED`
TCGA-2J-AAB4 TCGA-HZ-8005 TCGA-HZ-A4BH TCGA-IB-A5SQ TCGA-IB-A6UG 
       23.97         3.95         6.38         7.20         1.35 

$`RPL22 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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-A5SS TCGA-IB-A5ST TCGA-IB-A6UF TCGA-IB-A7LX TCGA-IB-A7M4 
       15.85        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-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RPL22 MUTATED RPL22 WILD-TYPE 
           1.35            0.03 
  RPL22 MUTATED RPL22 WILD-TYPE 
          23.97           75.12 
  RPL22 MUTATED RPL22 WILD-TYPE 
           6.38           14.47 
[1] "1.4 - 24.0 (6.4)"  "0.0 - 75.1 (14.5)"
[1] "hr=" "2.2"
D35V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RPL22 MUTATED          0        1         0         4         0        0
  RPL22 WILD-TYPE        3        7        23        99         4        4
D35V3, multiclass
           clus
vv          RPL22 MUTATED RPL22 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             0              23
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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
  RPL22 MUTATED     0   2     3
  RPL22 WILD-TYPE   4  14   122
D35V4, multiclass
       clus
vv      RPL22 MUTATED RPL22 WILD-TYPE
  T1                0               4
  T2                2              14
  T3+T4             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"
D35V5, binary
                 cls
clus                0   1
  RPL22 MUTATED     1   4
  RPL22 WILD-TYPE  36 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      1    4
  RPL22 WILD-TYPE   36  104
   clus
vv  RPL22 MUTATED RPL22 WILD-TYPE
  0             1              36
  1             4             104
[1] 2 2
[1] FALSE
D35V6, binary
                 cls
clus               0  1
  RPL22 MUTATED    3  0
  RPL22 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      3    0
  RPL22 WILD-TYPE   63    4
   clus
vv  RPL22 MUTATED RPL22 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D35V7, binary
                 cls
clus               0  1
  RPL22 MUTATED    1  4
  RPL22 WILD-TYPE 66 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      1    4
  RPL22 WILD-TYPE   66   75
        clus
vv       RPL22 MUTATED RPL22 WILD-TYPE
  FEMALE             1              66
  MALE               4              75
[1] 2 2
[1] FALSE
D35V8, binary
                 cls
clus               0  1
  RPL22 MUTATED    4  0
  RPL22 WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      4    0
  RPL22 WILD-TYPE   90   36
     clus
vv    RPL22 MUTATED RPL22 WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RPL22 MUTATED                                     4
  RPL22 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RPL22 MUTATED                                       1
  RPL22 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RPL22 MUTATED                                                  0
  RPL22 WILD-TYPE                                                2
D35V9, multiclass
                                                  clus
vv                                                 RPL22 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RPL22 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D35V10, continuous
[1] "Remove cluster labels:" "RPL22 MUTATED"         
clus
  RPL22 MUTATED RPL22 WILD-TYPE 
              1              49 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A7M4 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-YY-A8LH 
"RPL22 WILD-TYPE" 
D35V11, continuous
[1] "Remove cluster labels:" "RPL22 MUTATED"         
clus
  RPL22 MUTATED RPL22 WILD-TYPE 
              1              39 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RPL22 WILD-TYPE" "RPL22 WILD-TYPE" "RPL22 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RPL22 MUTATED    2  3  0  0
  RPL22 WILD-TYPE 77 47  4  3
D35V12, multiclass
    clus
vv   RPL22 MUTATED RPL22 WILD-TYPE
  R0             2              77
  R1             3              47
  R2             0               4
  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"
D35V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPL22 MUTATED       0                         0     5
  RPL22 WILD-TYPE     9                         5   123
D35V14, multiclass
                           clus
vv                          RPL22 MUTATED RPL22 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D35V15, binary
                 cls
clus                0   1
  RPL22 MUTATED     0   3
  RPL22 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL22 MUTATED      0    3
  RPL22 WILD-TYPE    5  102
                        clus
vv                       RPL22 MUTATED RPL22 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(36) Variable = NBPF16 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2               0  1
  NBPF16 MUTATED    2  5
  NBPF16 WILD-TYPE 66 71
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               7              137 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               5               71 
$`NBPF16 MUTATED`
TCGA-2J-AABV TCGA-2L-AAQE TCGA-FB-AAPU TCGA-HV-AA8X TCGA-IB-7897 TCGA-IB-AAUP 
       21.44        22.49        12.53        17.49        15.98        14.17 
TCGA-RB-AA9M 
        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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-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-A7B8 TCGA-S4-A8RM 
        8.78        15.45        13.68         3.12        15.32        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
        0.39        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  NBPF16 MUTATED NBPF16 WILD-TYPE 
            9.40             0.03 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
           22.49            75.12 
  NBPF16 MUTATED NBPF16 WILD-TYPE 
           15.98            14.14 
[1] "9.4 - 22.5 (16.0)" "0.0 - 75.1 (14.1)"
[1] "hr=" "1.3"
D36V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NBPF16 MUTATED          0        0         1         6         0        0
  NBPF16 WILD-TYPE        3        8        22        97         4        4
D36V3, multiclass
           clus
vv          NBPF16 MUTATED NBPF16 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              6               97
  STAGE III              0                4
  STAGE IV               0                4
[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   1     5
  NBPF16 WILD-TYPE   3  15   120
D36V4, multiclass
       clus
vv      NBPF16 MUTATED NBPF16 WILD-TYPE
  T1                 1                3
  T2                 1               15
  T3+T4              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"
D36V5, binary
                  cls
clus                 0   1
  NBPF16 MUTATED     1   6
  NBPF16 WILD-TYPE  36 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      1    6
  NBPF16 WILD-TYPE   36  102
   clus
vv  NBPF16 MUTATED NBPF16 WILD-TYPE
  0              1               36
  1              6              102
[1] 2 2
[1] FALSE
D36V6, binary
                  cls
clus                0  1
  NBPF16 MUTATED    4  0
  NBPF16 WILD-TYPE 62  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      4    0
  NBPF16 WILD-TYPE   62    4
   clus
vv  NBPF16 MUTATED NBPF16 WILD-TYPE
  0              4               62
  1              0                4
[1] 2 2
[1] FALSE
D36V7, binary
                  cls
clus                0  1
  NBPF16 MUTATED    3  4
  NBPF16 WILD-TYPE 64 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      3    4
  NBPF16 WILD-TYPE   64   75
        clus
vv       NBPF16 MUTATED NBPF16 WILD-TYPE
  FEMALE              3               64
  MALE                4               75
[1] 2 2
[1] FALSE
D36V8, binary
                  cls
clus                0  1
  NBPF16 MUTATED    6  1
  NBPF16 WILD-TYPE 88 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      6    1
  NBPF16 WILD-TYPE   88   35
     clus
vv    NBPF16 MUTATED NBPF16 WILD-TYPE
  NO               6               88
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NBPF16 MUTATED                                     7
  NBPF16 WILD-TYPE                                 123
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NBPF16 MUTATED                                       0
  NBPF16 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NBPF16 MUTATED                                                  0
  NBPF16 WILD-TYPE                                                2
D36V9, multiclass
                                                  clus
vv                                                 NBPF16 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 NBPF16 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D36V10, continuous
[1] "Remove cluster labels:" "NBPF16 MUTATED"        
clus
  NBPF16 MUTATED NBPF16 WILD-TYPE 
               2               48 
      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-HV-AA8V       TCGA-HZ-A77Q 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644       TCGA-IB-7649 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886       TCGA-IB-7887 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" "NBPF16 WILD-TYPE" 
D36V11, continuous
                  vv
clus               R0 R1 R2 RX
  NBPF16 MUTATED    3  3  1  0
  NBPF16 WILD-TYPE 76 47  3  3
D36V12, multiclass
    clus
vv   NBPF16 MUTATED NBPF16 WILD-TYPE
  R0              3               76
  R1              3               47
  R2              1                3
  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"
D36V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF16 MUTATED       2                         0     5
  NBPF16 WILD-TYPE     7                         5   123
D36V14, multiclass
                           clus
vv                          NBPF16 MUTATED NBPF16 WILD-TYPE
  ASIAN                                  2                7
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              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"
D36V15, binary
                  cls
clus                 0   1
  NBPF16 MUTATED     0   4
  NBPF16 WILD-TYPE   5 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF16 MUTATED      0    4
  NBPF16 WILD-TYPE    5  101
                        clus
vv                       NBPF16 MUTATED NBPF16 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              101
[1] 2 2
[1] FALSE

Clustering(37) Variable = CD86 MUTATION ANALYSIS
D37V1, survival
                sevent
clus2             0  1
  CD86 MUTATED    4  2
  CD86 WILD-TYPE 64 74
  CD86 MUTATED CD86 WILD-TYPE 
             6            138 
  CD86 MUTATED CD86 WILD-TYPE 
             2             74 
$`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        24.23 

$`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        42.31        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        58.98        43.50        20.84         7.36        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7885 
       12.95        49.38         4.77        21.90        15.35        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-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         9.44        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-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
        9.40        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  CD86 MUTATED CD86 WILD-TYPE 
          8.05           0.03 
  CD86 MUTATED CD86 WILD-TYPE 
         24.26          75.12 
  CD86 MUTATED CD86 WILD-TYPE 
         21.81          13.99 
[1] "8.1 - 24.3 (21.8)" "0.0 - 75.1 (14.0)"
[1] "hr=" "2.4"
D37V2, 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        3        8        22        98         4        4
D37V3, multiclass
           clus
vv          CD86 MUTATED CD86 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            1             22
  STAGE IIB            5             98
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   119
D37V4, multiclass
       clus
vv      CD86 MUTATED CD86 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D37V5, binary
                cls
clus               0   1
  CD86 MUTATED     1   5
  CD86 WILD-TYPE  36 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      1    5
  CD86 WILD-TYPE   36  103
   clus
vv  CD86 MUTATED CD86 WILD-TYPE
  0            1             36
  1            5            103
[1] 2 2
[1] FALSE
D37V6, binary
                cls
clus              0  1
  CD86 MUTATED    4  0
  CD86 WILD-TYPE 62  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      4    0
  CD86 WILD-TYPE   62    4
   clus
vv  CD86 MUTATED CD86 WILD-TYPE
  0            4             62
  1            0              4
[1] 2 2
[1] FALSE
D37V7, binary
                cls
clus              0  1
  CD86 MUTATED    3  3
  CD86 WILD-TYPE 64 76
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      3    3
  CD86 WILD-TYPE   64   76
        clus
vv       CD86 MUTATED CD86 WILD-TYPE
  FEMALE            3             64
  MALE              3             76
[1] 2 2
[1] FALSE
D37V8, binary
                cls
clus              0  1
  CD86 MUTATED    5  1
  CD86 WILD-TYPE 89 35
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      5    1
  CD86 WILD-TYPE   89   35
     clus
vv    CD86 MUTATED CD86 WILD-TYPE
  NO             5             89
  YES            1             35
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD86 MUTATED                                     6
  CD86 WILD-TYPE                                 124
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD86 MUTATED                                       0
  CD86 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD86 MUTATED                                                  0
  CD86 WILD-TYPE                                                2
D37V9, multiclass
                                                  clus
vv                                                 CD86 MUTATED CD86 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6            124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D37V10, continuous
D37V11, continuous
[1] "Remove cluster labels:" "CD86 MUTATED"          
clus
  CD86 MUTATED CD86 WILD-TYPE 
             2             38 
    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-XN-A8T5     TCGA-YY-A8LH 
"CD86 WILD-TYPE" "CD86 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CD86 MUTATED    4  2  0  0
  CD86 WILD-TYPE 75 48  4  3
D37V12, multiclass
    clus
vv   CD86 MUTATED CD86 WILD-TYPE
  R0            4             75
  R1            2             48
  R2            0              4
  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"
D37V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD86 MUTATED       1                         0     5
  CD86 WILD-TYPE     8                         5   123
D37V14, multiclass
                           clus
vv                          CD86 MUTATED CD86 WILD-TYPE
  ASIAN                                1              8
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            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"
D37V15, binary
                cls
clus              0  1
  CD86 MUTATED    0  6
  CD86 WILD-TYPE  5 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD86 MUTATED      0    6
  CD86 WILD-TYPE    5   99
                        clus
vv                       CD86 MUTATED CD86 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             99
[1] 2 2
[1] FALSE

Clustering(38) Variable = PARP10 MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2               0  1
  PARP10 MUTATED    3  2
  PARP10 WILD-TYPE 65 74
  PARP10 MUTATED PARP10 WILD-TYPE 
               5              139 
  PARP10 MUTATED PARP10 WILD-TYPE 
               2               74 
$`PARP10 MUTATED`
TCGA-3A-A9IH TCGA-HZ-7922 TCGA-IB-7651 TCGA-IB-7887 TCGA-Z5-AAPL 
       33.57         0.13        19.82         3.62        15.35 

$`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        42.31        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        58.98        43.50        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        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  PARP10 MUTATED PARP10 WILD-TYPE 
            0.13             0.03 
  PARP10 MUTATED PARP10 WILD-TYPE 
           33.57            75.12 
  PARP10 MUTATED PARP10 WILD-TYPE 
           15.35            14.17 
[1] "0.1 - 33.6 (15.3)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.2"
D38V2, 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        2        8        22       100         4        4
D38V3, multiclass
           clus
vv          PARP10 MUTATED PARP10 WILD-TYPE
  STAGE IA               1                2
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   3  16   121
D38V4, multiclass
       clus
vv      PARP10 MUTATED PARP10 WILD-TYPE
  T1                 1                3
  T2                 0               16
  T3+T4              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"
D38V5, binary
                  cls
clus                 0   1
  PARP10 MUTATED     2   3
  PARP10 WILD-TYPE  35 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP10 MUTATED      2    3
  PARP10 WILD-TYPE   35  105
   clus
vv  PARP10 MUTATED PARP10 WILD-TYPE
  0              2               35
  1              3              105
[1] 2 2
[1] FALSE
D38V6, binary
                  cls
clus                0  1
  PARP10 MUTATED    3  0
  PARP10 WILD-TYPE 63  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP10 MUTATED      3    0
  PARP10 WILD-TYPE   63    4
   clus
vv  PARP10 MUTATED PARP10 WILD-TYPE
  0              3               63
  1              0                4
[1] 2 2
[1] FALSE
D38V7, binary
                  cls
clus                0  1
  PARP10 MUTATED    5  0
  PARP10 WILD-TYPE 62 79
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP10 MUTATED      5    0
  PARP10 WILD-TYPE   62   79
        clus
vv       PARP10 MUTATED PARP10 WILD-TYPE
  FEMALE              5               62
  MALE                0               79
[1] 2 2
[1] FALSE
D38V8, binary
                  cls
clus                0  1
  PARP10 MUTATED    4  0
  PARP10 WILD-TYPE 90 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP10 MUTATED      4    0
  PARP10 WILD-TYPE   90   36
     clus
vv    PARP10 MUTATED PARP10 WILD-TYPE
  NO               4               90
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PARP10 MUTATED                                     5
  PARP10 WILD-TYPE                                 125
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PARP10 MUTATED                                       0
  PARP10 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PARP10 MUTATED                                                  0
  PARP10 WILD-TYPE                                                2
D38V9, 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                           125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D38V10, continuous
[1] "Remove cluster labels:" "PARP10 MUTATED"        
clus
  PARP10 MUTATED PARP10 WILD-TYPE 
               2               48 
      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-HV-AA8V       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-IB-AAUU       TCGA-LB-A7SX 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
D38V11, continuous
[1] "Remove cluster labels:" "PARP10 MUTATED"        
clus
  PARP10 MUTATED PARP10 WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"PARP10 WILD-TYPE" "PARP10 WILD-TYPE" "PARP10 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PARP10 MUTATED    4  1  0  0
  PARP10 WILD-TYPE 75 49  4  3
D38V12, multiclass
    clus
vv   PARP10 MUTATED PARP10 WILD-TYPE
  R0              4               75
  R1              1               49
  R2              0                4
  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"
D38V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PARP10 MUTATED       0                         0     5
  PARP10 WILD-TYPE     9                         5   123
D38V14, multiclass
                           clus
vv                          PARP10 MUTATED PARP10 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              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"
D38V15, binary
                  cls
clus                 0   1
  PARP10 MUTATED     0   5
  PARP10 WILD-TYPE   5 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP10 MUTATED      0    5
  PARP10 WILD-TYPE    5  100
                        clus
vv                       PARP10 MUTATED PARP10 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5              100
[1] 2 2
[1] FALSE

Clustering(39) Variable = VWA3A MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2              0  1
  VWA3A MUTATED    1  4
  VWA3A WILD-TYPE 67 72
  VWA3A MUTATED VWA3A WILD-TYPE 
              5             139 
  VWA3A MUTATED VWA3A WILD-TYPE 
              4              72 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         3.95         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       14.93        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7645 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  VWA3A MUTATED VWA3A WILD-TYPE 
           2.63            0.03 
  VWA3A MUTATED VWA3A WILD-TYPE 
          19.82           75.12 
  VWA3A MUTATED VWA3A WILD-TYPE 
          12.95           14.40 
[1] "2.6 - 19.8 (12.9)" "0.0 - 75.1 (14.4)"
[1] "hr=" "2"  
D39V2, 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        3        8        23       100         4        2
D39V3, multiclass
           clus
vv          VWA3A MUTATED VWA3A WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              2               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
  VWA3A MUTATED     0   0     5
  VWA3A WILD-TYPE   4  16   120
D39V4, multiclass
       clus
vv      VWA3A MUTATED VWA3A WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D39V5, binary
                 cls
clus                0   1
  VWA3A MUTATED     1   4
  VWA3A WILD-TYPE  36 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      1    4
  VWA3A WILD-TYPE   36  104
   clus
vv  VWA3A MUTATED VWA3A WILD-TYPE
  0             1              36
  1             4             104
[1] 2 2
[1] FALSE
D39V6, binary
                 cls
clus               0  1
  VWA3A MUTATED    2  2
  VWA3A WILD-TYPE 64  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      2    2
  VWA3A WILD-TYPE   64    2
   clus
vv  VWA3A MUTATED VWA3A WILD-TYPE
  0             2              64
  1             2               2
[1] 2 2
[1] FALSE
D39V7, binary
                 cls
clus               0  1
  VWA3A MUTATED    3  2
  VWA3A WILD-TYPE 64 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      3    2
  VWA3A WILD-TYPE   64   77
        clus
vv       VWA3A MUTATED VWA3A WILD-TYPE
  FEMALE             3              64
  MALE               2              77
[1] 2 2
[1] FALSE
D39V8, binary
                 cls
clus               0  1
  VWA3A MUTATED    3  0
  VWA3A WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      3    0
  VWA3A WILD-TYPE   91   36
     clus
vv    VWA3A MUTATED VWA3A WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  VWA3A MUTATED                                     5
  VWA3A WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  VWA3A MUTATED                                       0
  VWA3A WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  VWA3A MUTATED                                                  0
  VWA3A WILD-TYPE                                                2
D39V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D39V10, continuous
[1] "Remove cluster labels:" "VWA3A MUTATED"         
clus
  VWA3A MUTATED VWA3A WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
D39V11, continuous
[1] "Remove cluster labels:" "VWA3A MUTATED"         
clus
  VWA3A MUTATED VWA3A WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"VWA3A WILD-TYPE" "VWA3A WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  VWA3A MUTATED    2  3  0  0
  VWA3A WILD-TYPE 77 47  4  3
D39V12, multiclass
    clus
vv   VWA3A MUTATED VWA3A WILD-TYPE
  R0             2              77
  R1             3              47
  R2             0               4
  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"
D39V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VWA3A MUTATED       0                         0     5
  VWA3A WILD-TYPE     9                         5   123
D39V14, multiclass
                           clus
vv                          VWA3A MUTATED VWA3A WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D39V15, binary
                 cls
clus                0   1
  VWA3A MUTATED     0   4
  VWA3A WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA3A MUTATED      0    4
  VWA3A WILD-TYPE    5  101
                        clus
vv                       VWA3A MUTATED VWA3A WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(40) Variable = SHROOM4 MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  SHROOM4 MUTATED    4  6
  SHROOM4 WILD-TYPE 64 70
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               10               134 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                6                70 
$`SHROOM4 MUTATED`
TCGA-3A-A9I5 TCGA-FB-AAPU TCGA-HZ-7922 TCGA-HZ-8002 TCGA-HZ-8315 TCGA-HZ-A49I 
       58.98        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        42.31        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        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       30.25        17.49        19.50        20.19        17.03        23.21 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G 
       19.59         3.95        12.43        14.93        17.92        21.70 
TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
       16.14        21.60         5.26        10.85         1.08         0.23 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        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-7893 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
       19.66         3.85         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             0.13              0.03 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
            58.98             75.12 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
           12.280            14.435 
[1] "0.1 - 59.0 (12.3)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SHROOM4 MUTATED          0        0         2         8         0        0
  SHROOM4 WILD-TYPE        3        8        21        95         4        4
D40V3, multiclass
           clus
vv          SHROOM4 MUTATED SHROOM4 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               2                21
  STAGE IIB               8                95
  STAGE III               0                 4
  STAGE IV                0                 4
[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     0   0    10
  SHROOM4 WILD-TYPE   4  16   115
D40V4, multiclass
       clus
vv      SHROOM4 MUTATED SHROOM4 WILD-TYPE
  T1                  0                 4
  T2                  0                16
  T3+T4              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"
D40V5, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED     3   8
  SHROOM4 WILD-TYPE  34 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      3    8
  SHROOM4 WILD-TYPE   34  100
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0               3                34
  1               8               100
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    3  0
  SHROOM4 WILD-TYPE 63  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      3    0
  SHROOM4 WILD-TYPE   63    4
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0               3                63
  1               0                 4
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    7  4
  SHROOM4 WILD-TYPE 60 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      7    4
  SHROOM4 WILD-TYPE   60   75
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  FEMALE               7                60
  MALE                 4                75
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    5  2
  SHROOM4 WILD-TYPE 89 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      5    2
  SHROOM4 WILD-TYPE   89   34
     clus
vv    SHROOM4 MUTATED SHROOM4 WILD-TYPE
  NO                5                89
  YES               2                34
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SHROOM4 MUTATED                                    11
  SHROOM4 WILD-TYPE                                 119
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SHROOM4 MUTATED                                       0
  SHROOM4 WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SHROOM4 MUTATED                                                  0
  SHROOM4 WILD-TYPE                                                2
D40V9, 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                            119
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D40V10, continuous
[1] "Remove cluster labels:" "SHROOM4 MUTATED"       
clus
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                2                48 
       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-HV-AA8V        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-7887        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
D40V11, continuous
[1] "Remove cluster labels:" "SHROOM4 MUTATED"       
clus
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                2                38 
       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-XN-A8T5        TCGA-YY-A8LH 
"SHROOM4 WILD-TYPE" "SHROOM4 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  SHROOM4 MUTATED    7  4  0  0
  SHROOM4 WILD-TYPE 72 46  4  3
D40V12, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  R0               7                72
  R1               4                46
  R2               0                 4
  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"
D40V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SHROOM4 MUTATED       1                         0    10
  SHROOM4 WILD-TYPE     8                         5   118
D40V14, multiclass
                           clus
vv                          SHROOM4 MUTATED SHROOM4 WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                  10               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"
D40V15, binary
                   cls
clus                 0  1
  SHROOM4 MUTATED    1  9
  SHROOM4 WILD-TYPE  4 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED      1    9
  SHROOM4 WILD-TYPE    4   96
                        clus
vv                       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               9                96
[1] 2 2
[1] FALSE

Clustering(41) Variable = PRKRA MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2              0  1
  PRKRA MUTATED    2  2
  PRKRA WILD-TYPE 66 74
  PRKRA MUTATED PRKRA WILD-TYPE 
              4             140 
  PRKRA MUTATED PRKRA WILD-TYPE 
              2              74 
$`PRKRA MUTATED`
TCGA-FB-AAQ1 TCGA-HV-A5A4 TCGA-IB-7891 TCGA-RB-A7B8 
        4.04         7.63        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       12.89        13.84         4.21         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       19.66         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PRKRA MUTATED PRKRA WILD-TYPE 
           4.04            0.03 
  PRKRA MUTATED PRKRA WILD-TYPE 
          21.30           75.12 
  PRKRA MUTATED PRKRA WILD-TYPE 
         11.475          14.285 
[1] "4.0 - 21.3 (11.5)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.3"
D41V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PRKRA MUTATED          0        0         1         3         0        0
  PRKRA WILD-TYPE        3        8        22       100         4        4
D41V3, multiclass
           clus
vv          PRKRA MUTATED PRKRA WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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     4
  PRKRA WILD-TYPE   4  16   121
D41V4, multiclass
       clus
vv      PRKRA MUTATED PRKRA WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D41V5, binary
                 cls
clus                0   1
  PRKRA MUTATED     1   3
  PRKRA WILD-TYPE  36 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKRA MUTATED      1    3
  PRKRA WILD-TYPE   36  105
   clus
vv  PRKRA MUTATED PRKRA WILD-TYPE
  0             1              36
  1             3             105
[1] 2 2
[1] FALSE
D41V6, binary
                 cls
clus               0  1
  PRKRA MUTATED    1  0
  PRKRA WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKRA MUTATED      1    0
  PRKRA WILD-TYPE   65    4
   clus
vv  PRKRA MUTATED PRKRA WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D41V7, binary
                 cls
clus               0  1
  PRKRA MUTATED    3  1
  PRKRA WILD-TYPE 64 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKRA MUTATED      3    1
  PRKRA WILD-TYPE   64   78
        clus
vv       PRKRA MUTATED PRKRA WILD-TYPE
  FEMALE             3              64
  MALE               1              78
[1] 2 2
[1] FALSE
D41V8, binary
                 cls
clus               0  1
  PRKRA MUTATED    4  0
  PRKRA WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKRA MUTATED      4    0
  PRKRA WILD-TYPE   90   36
     clus
vv    PRKRA MUTATED PRKRA WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRKRA MUTATED                                     3
  PRKRA WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRKRA MUTATED                                       1
  PRKRA WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRKRA MUTATED                                                  0
  PRKRA WILD-TYPE                                                2
D41V9, multiclass
                                                  clus
vv                                                 PRKRA MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PRKRA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D41V10, continuous
[1] "Remove cluster labels:" "PRKRA MUTATED"         
clus
  PRKRA MUTATED PRKRA WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-8126      TCGA-IB-8127 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
     TCGA-YY-A8LH 
"PRKRA WILD-TYPE" 
D41V11, continuous
[1] "Remove cluster labels:" "PRKRA MUTATED"         
clus
  PRKRA MUTATED PRKRA WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"PRKRA WILD-TYPE" "PRKRA WILD-TYPE" "PRKRA WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PRKRA MUTATED    2  1  0  0
  PRKRA WILD-TYPE 77 49  4  3
D41V12, multiclass
    clus
vv   PRKRA MUTATED PRKRA WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D41V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRKRA MUTATED       1                         0     3
  PRKRA WILD-TYPE     8                         5   125
D41V14, multiclass
                           clus
vv                          PRKRA MUTATED PRKRA WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, binary
                 cls
clus                0   1
  PRKRA MUTATED     0   3
  PRKRA WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKRA MUTATED      0    3
  PRKRA WILD-TYPE    5  102
                        clus
vv                       PRKRA MUTATED PRKRA WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(42) Variable = RBM12 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2              0  1
  RBM12 MUTATED    2  3
  RBM12 WILD-TYPE 66 73
  RBM12 MUTATED RBM12 WILD-TYPE 
              5             139 
  RBM12 MUTATED RBM12 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       33.57        15.06        34.09        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-AAUQ 
        8.22        15.88         0.26         4.73         7.86         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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RBM12 MUTATED RBM12 WILD-TYPE 
           1.02            0.03 
  RBM12 MUTATED RBM12 WILD-TYPE 
          17.00           75.12 
  RBM12 MUTATED RBM12 WILD-TYPE 
          14.17           14.40 
[1] "1.0 - 17.0 (14.2)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.8"
D42V2, 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        3        8        22        99         4        4
D42V3, multiclass
           clus
vv          RBM12 MUTATED RBM12 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   120
D42V4, multiclass
       clus
vv      RBM12 MUTATED RBM12 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D42V5, binary
                 cls
clus                0   1
  RBM12 MUTATED     1   4
  RBM12 WILD-TYPE  36 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      1    4
  RBM12 WILD-TYPE   36  104
   clus
vv  RBM12 MUTATED RBM12 WILD-TYPE
  0             1              36
  1             4             104
[1] 2 2
[1] FALSE
D42V6, binary
                 cls
clus               0  1
  RBM12 MUTATED    2  0
  RBM12 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      2    0
  RBM12 WILD-TYPE   64    4
   clus
vv  RBM12 MUTATED RBM12 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D42V7, binary
                 cls
clus               0  1
  RBM12 MUTATED    2  3
  RBM12 WILD-TYPE 65 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      2    3
  RBM12 WILD-TYPE   65   76
        clus
vv       RBM12 MUTATED RBM12 WILD-TYPE
  FEMALE             2              65
  MALE               3              76
[1] 2 2
[1] FALSE
D42V8, binary
                 cls
clus               0  1
  RBM12 MUTATED    5  0
  RBM12 WILD-TYPE 89 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      5    0
  RBM12 WILD-TYPE   89   36
     clus
vv    RBM12 MUTATED RBM12 WILD-TYPE
  NO              5              89
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM12 MUTATED                                     4
  RBM12 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM12 MUTATED                                       1
  RBM12 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM12 MUTATED                                                  0
  RBM12 WILD-TYPE                                                2
D42V9, 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                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D42V10, continuous
[1] "Remove cluster labels:" "RBM12 MUTATED"         
clus
  RBM12 MUTATED RBM12 WILD-TYPE 
              1              49 
     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-HV-AA8V 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" "RBM12 WILD-TYPE" 
     TCGA-YY-A8LH 
"RBM12 WILD-TYPE" 
D42V11, continuous
                 vv
clus              R0 R1 R2 RX
  RBM12 MUTATED    2  3  0  0
  RBM12 WILD-TYPE 77 47  4  3
D42V12, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  R0             2              77
  R1             3              47
  R2             0               4
  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"
D42V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM12 MUTATED       0                         0     5
  RBM12 WILD-TYPE     9                         5   123
D42V14, multiclass
                           clus
vv                          RBM12 MUTATED RBM12 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D42V15, binary
                 cls
clus                0   1
  RBM12 MUTATED     1   4
  RBM12 WILD-TYPE   4 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      1    4
  RBM12 WILD-TYPE    4  101
                        clus
vv                       RBM12 MUTATED RBM12 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(43) Variable = ZNF880 MUTATION ANALYSIS
D43V1, survival
                  sevent
clus2               0  1
  ZNF880 MUTATED    1  3
  ZNF880 WILD-TYPE 67 73
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               4              140 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               3               73 
$`ZNF880 MUTATED`
TCGA-2L-AAQI TCGA-HZ-8315 TCGA-HZ-A9TJ TCGA-IB-7897 
        3.39         9.83        19.82        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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8317 
       17.03        23.21        12.03        19.59         3.95        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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZNF880 MUTATED ZNF880 WILD-TYPE 
            3.39             0.03 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
           19.82            75.12 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
          12.905           14.285 
[1] "3.4 - 19.8 (12.9)" "0.0 - 75.1 (14.3)"
[1] "hr=" "2"  
D43V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZNF880 MUTATED          0        0         1         2         0        1
  ZNF880 WILD-TYPE        3        8        22       101         4        3
D43V3, multiclass
           clus
vv          ZNF880 MUTATED ZNF880 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              2              101
  STAGE III              0                4
  STAGE IV               1                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     4
  ZNF880 WILD-TYPE   4  16   121
D43V4, multiclass
       clus
vv      ZNF880 MUTATED ZNF880 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D43V5, binary
                  cls
clus                 0   1
  ZNF880 MUTATED     2   2
  ZNF880 WILD-TYPE  35 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      2    2
  ZNF880 WILD-TYPE   35  106
   clus
vv  ZNF880 MUTATED ZNF880 WILD-TYPE
  0              2               35
  1              2              106
[1] 2 2
[1] FALSE
D43V6, binary
                  cls
clus                0  1
  ZNF880 MUTATED    1  1
  ZNF880 WILD-TYPE 65  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      1    1
  ZNF880 WILD-TYPE   65    3
   clus
vv  ZNF880 MUTATED ZNF880 WILD-TYPE
  0              1               65
  1              1                3
[1] 2 2
[1] FALSE
D43V7, binary
                  cls
clus                0  1
  ZNF880 MUTATED    2  2
  ZNF880 WILD-TYPE 65 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      2    2
  ZNF880 WILD-TYPE   65   77
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  FEMALE              2               65
  MALE                2               77
[1] 2 2
[1] FALSE
D43V8, binary
                  cls
clus                0  1
  ZNF880 MUTATED    3  0
  ZNF880 WILD-TYPE 91 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      3    0
  ZNF880 WILD-TYPE   91   36
     clus
vv    ZNF880 MUTATED ZNF880 WILD-TYPE
  NO               3               91
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF880 MUTATED                                     3
  ZNF880 WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF880 MUTATED                                       1
  ZNF880 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF880 MUTATED                                                  0
  ZNF880 WILD-TYPE                                                2
D43V9, multiclass
                                                  clus
vv                                                 ZNF880 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ZNF880 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D43V10, continuous
D43V11, continuous
                  vv
clus               R0 R1 R2 RX
  ZNF880 MUTATED    2  2  0  0
  ZNF880 WILD-TYPE 77 48  4  3
D43V12, multiclass
    clus
vv   ZNF880 MUTATED ZNF880 WILD-TYPE
  R0              2               77
  R1              2               48
  R2              0                4
  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"
D43V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF880 MUTATED       0                         0     4
  ZNF880 WILD-TYPE     9                         5   124
D43V14, multiclass
                           clus
vv                          ZNF880 MUTATED ZNF880 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
                  cls
clus                 0   1
  ZNF880 MUTATED     0   3
  ZNF880 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      0    3
  ZNF880 WILD-TYPE    5  102
                        clus
vv                       ZNF880 MUTATED ZNF880 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(44) Variable = CDC27 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    3  4
  CDC27 WILD-TYPE 65 72
  CDC27 MUTATED CDC27 WILD-TYPE 
              7             137 
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              72 
$`CDC27 MUTATED`
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-FB-AAPY TCGA-HZ-7926 TCGA-IB-AAUP TCGA-LB-A8F3 
       43.50        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        42.31        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        58.98         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 
       17.49        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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-AAUQ TCGA-IB-AAUR 
       15.88         0.26         4.73         7.86         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-A779 
       24.23        17.26        23.08        22.85        39.98        16.80 
TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUL TCGA-XN-A8T3 
       14.14         0.39        13.81        12.99        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  CDC27 MUTATED CDC27 WILD-TYPE 
          12.03            0.03 
  CDC27 MUTATED CDC27 WILD-TYPE 
          43.50           75.12 
  CDC27 MUTATED CDC27 WILD-TYPE 
          17.03           14.14 
[1] "12.0 - 43.5 (17.0)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "1.2"
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        3        8        21        98         4        4
D44V3, multiclass
           clus
vv          CDC27 MUTATED CDC27 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             2              21
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              0               4
[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   4  15   119
D44V4, multiclass
       clus
vv      CDC27 MUTATED CDC27 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D44V5, binary
                 cls
clus                0   1
  CDC27 MUTATED     2   5
  CDC27 WILD-TYPE  35 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    5
  CDC27 WILD-TYPE   35  103
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             2              35
  1             5             103
[1] 2 2
[1] FALSE
D44V6, binary
                 cls
clus               0  1
  CDC27 MUTATED    1  0
  CDC27 WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      1    0
  CDC27 WILD-TYPE   65    4
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D44V7, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  5
  CDC27 WILD-TYPE 65 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    5
  CDC27 WILD-TYPE   65   74
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             2              65
  MALE               5              74
[1] 2 2
[1] FALSE
D44V8, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  4
  CDC27 WILD-TYPE 92 32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    4
  CDC27 WILD-TYPE   92   32
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  NO              2              92
  YES             4              32
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDC27 MUTATED                                     7
  CDC27 WILD-TYPE                                 123
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDC27 MUTATED                                       0
  CDC27 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDC27 MUTATED                                                  0
  CDC27 WILD-TYPE                                                2
D44V9, 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                          123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D44V10, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              2              48 
     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-HV-AA8V      TCGA-HZ-A77Q 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644      TCGA-IB-7649 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886      TCGA-IB-7887 
"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-IB-AAUU      TCGA-LB-A7SX 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
D44V11, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CDC27 MUTATED    4  2  0  1
  CDC27 WILD-TYPE 75 48  4  2
D44V12, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  R0             4              75
  R1             2              48
  R2             0               4
  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"
D44V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED       0                         3     4
  CDC27 WILD-TYPE     9                         2   124
D44V14, multiclass
                           clus
vv                          CDC27 MUTATED CDC27 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             3               2
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, binary
                 cls
clus               0  1
  CDC27 MUTATED    0  7
  CDC27 WILD-TYPE  5 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      0    7
  CDC27 WILD-TYPE    5   98
                        clus
vv                       CDC27 MUTATED CDC27 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              98
[1] 2 2
[1] FALSE

Clustering(45) Variable = SUZ12 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2              0  1
  SUZ12 MUTATED    1  3
  SUZ12 WILD-TYPE 67 73
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              4             140 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SUZ12 MUTATED SUZ12 WILD-TYPE 
          10.98            0.03 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
          41.33           75.12 
  SUZ12 MUTATED SUZ12 WILD-TYPE 
         20.005          14.155 
[1] "11.0 - 41.3 (20.0)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "1"  
D45V2, 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        3        8        23        99         4        4
D45V3, multiclass
           clus
vv          SUZ12 MUTATED SUZ12 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   121
D45V4, multiclass
       clus
vv      SUZ12 MUTATED SUZ12 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D45V5, binary
                 cls
clus                0   1
  SUZ12 MUTATED     0   4
  SUZ12 WILD-TYPE  37 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      0    4
  SUZ12 WILD-TYPE   37  104
   clus
vv  SUZ12 MUTATED SUZ12 WILD-TYPE
  0             0              37
  1             4             104
[1] 2 2
[1] FALSE
D45V6, binary
                 cls
clus               0  1
  SUZ12 MUTATED    3  0
  SUZ12 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      3    0
  SUZ12 WILD-TYPE   63    4
   clus
vv  SUZ12 MUTATED SUZ12 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D45V7, binary
                 cls
clus               0  1
  SUZ12 MUTATED    2  2
  SUZ12 WILD-TYPE 65 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      2    2
  SUZ12 WILD-TYPE   65   77
        clus
vv       SUZ12 MUTATED SUZ12 WILD-TYPE
  FEMALE             2              65
  MALE               2              77
[1] 2 2
[1] FALSE
D45V8, binary
                 cls
clus               0  1
  SUZ12 MUTATED    4  0
  SUZ12 WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      4    0
  SUZ12 WILD-TYPE   90   36
     clus
vv    SUZ12 MUTATED SUZ12 WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SUZ12 MUTATED                                     3
  SUZ12 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SUZ12 MUTATED                                       1
  SUZ12 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SUZ12 MUTATED                                                  0
  SUZ12 WILD-TYPE                                                2
D45V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D45V10, continuous
[1] "Remove cluster labels:" "SUZ12 MUTATED"         
clus
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
D45V11, continuous
[1] "Remove cluster labels:" "SUZ12 MUTATED"         
clus
  SUZ12 MUTATED SUZ12 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"SUZ12 WILD-TYPE" "SUZ12 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SUZ12 MUTATED    4  0  0  0
  SUZ12 WILD-TYPE 75 50  4  3
D45V12, multiclass
    clus
vv   SUZ12 MUTATED SUZ12 WILD-TYPE
  R0             4              75
  R1             0              50
  R2             0               4
  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"
D45V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SUZ12 MUTATED       0                         0     4
  SUZ12 WILD-TYPE     9                         5   124
D45V14, multiclass
                           clus
vv                          SUZ12 MUTATED SUZ12 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                 cls
clus                0   1
  SUZ12 MUTATED     0   3
  SUZ12 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUZ12 MUTATED      0    3
  SUZ12 WILD-TYPE    5  102
                        clus
vv                       SUZ12 MUTATED SUZ12 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(46) Variable = SORBS2 MUTATION ANALYSIS
D46V1, survival
                  sevent
clus2               0  1
  SORBS2 MUTATED    2  3
  SORBS2 WILD-TYPE 66 73
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               5              139 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               3               73 
$`SORBS2 MUTATED`
TCGA-F2-A8YN TCGA-FB-AAPU TCGA-HV-AA8V TCGA-IB-7651 TCGA-RB-A7B8 
       17.00        12.53        30.25        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SORBS2 MUTATED SORBS2 WILD-TYPE 
           12.53             0.03 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           30.25            75.12 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           17.00            14.14 
[1] "12.5 - 30.2 (17.0)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "1.1"
D46V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SORBS2 MUTATED          0        0         2         4         0        0
  SORBS2 WILD-TYPE        3        8        21        99         4        4
D46V3, multiclass
           clus
vv          SORBS2 MUTATED SORBS2 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              2               21
  STAGE IIB              4               99
  STAGE III              0                4
  STAGE IV               0                4
[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     6
  SORBS2 WILD-TYPE   4  16   119
D46V4, multiclass
       clus
vv      SORBS2 MUTATED SORBS2 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D46V5, binary
                  cls
clus                 0   1
  SORBS2 MUTATED     2   4
  SORBS2 WILD-TYPE  35 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      2    4
  SORBS2 WILD-TYPE   35  104
   clus
vv  SORBS2 MUTATED SORBS2 WILD-TYPE
  0              2               35
  1              4              104
[1] 2 2
[1] FALSE
D46V6, binary
                  cls
clus                0  1
  SORBS2 MUTATED    2  0
  SORBS2 WILD-TYPE 64  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      2    0
  SORBS2 WILD-TYPE   64    4
   clus
vv  SORBS2 MUTATED SORBS2 WILD-TYPE
  0              2               64
  1              0                4
[1] 2 2
[1] FALSE
D46V7, binary
                  cls
clus                0  1
  SORBS2 MUTATED    3  3
  SORBS2 WILD-TYPE 64 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      3    3
  SORBS2 WILD-TYPE   64   76
        clus
vv       SORBS2 MUTATED SORBS2 WILD-TYPE
  FEMALE              3               64
  MALE                3               76
[1] 2 2
[1] FALSE
D46V8, binary
                  cls
clus                0  1
  SORBS2 MUTATED    5  0
  SORBS2 WILD-TYPE 89 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      5    0
  SORBS2 WILD-TYPE   89   36
     clus
vv    SORBS2 MUTATED SORBS2 WILD-TYPE
  NO               5               89
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SORBS2 MUTATED                                     5
  SORBS2 WILD-TYPE                                 125
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SORBS2 MUTATED                                       1
  SORBS2 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SORBS2 MUTATED                                                  0
  SORBS2 WILD-TYPE                                                2
D46V9, multiclass
                                                  clus
vv                                                 SORBS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 SORBS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D46V10, continuous
D46V11, continuous
[1] "Remove cluster labels:" "SORBS2 MUTATED"        
clus
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"SORBS2 WILD-TYPE" "SORBS2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  SORBS2 MUTATED    3  2  1  0
  SORBS2 WILD-TYPE 76 48  3  3
D46V12, multiclass
    clus
vv   SORBS2 MUTATED SORBS2 WILD-TYPE
  R0              3               76
  R1              2               48
  R2              1                3
  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"
D46V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SORBS2 MUTATED       2                         0     4
  SORBS2 WILD-TYPE     7                         5   124
D46V14, multiclass
                           clus
vv                          SORBS2 MUTATED SORBS2 WILD-TYPE
  ASIAN                                  2                7
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                  cls
clus                 0   1
  SORBS2 MUTATED     0   5
  SORBS2 WILD-TYPE   5 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      0    5
  SORBS2 WILD-TYPE    5  100
                        clus
vv                       SORBS2 MUTATED SORBS2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5              100
[1] 2 2
[1] FALSE

Clustering(47) Variable = RNF32 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2              0  1
  RNF32 MUTATED    1  4
  RNF32 WILD-TYPE 67 72
  RNF32 MUTATED RNF32 WILD-TYPE 
              5             139 
  RNF32 MUTATED RNF32 WILD-TYPE 
              4              72 
$`RNF32 MUTATED`
TCGA-HZ-7925 TCGA-HZ-8002 TCGA-HZ-8005 TCGA-IB-7651 TCGA-XN-A8T3 
       20.19        12.03         3.95        19.82        31.27 

$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       17.03        23.21        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        16.37        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RNF32 MUTATED RNF32 WILD-TYPE 
           3.95            0.03 
  RNF32 MUTATED RNF32 WILD-TYPE 
          31.27           75.12 
  RNF32 MUTATED RNF32 WILD-TYPE 
          19.82           14.17 
[1] "4.0 - 31.3 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.4"
D47V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RNF32 MUTATED          0        1         0         4         0        0
  RNF32 WILD-TYPE        3        7        23        99         4        4
D47V3, multiclass
           clus
vv          RNF32 MUTATED RNF32 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             0              23
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   1     4
  RNF32 WILD-TYPE   4  15   121
D47V4, multiclass
       clus
vv      RNF32 MUTATED RNF32 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D47V5, binary
                 cls
clus                0   1
  RNF32 MUTATED     1   4
  RNF32 WILD-TYPE  36 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF32 MUTATED      1    4
  RNF32 WILD-TYPE   36  104
   clus
vv  RNF32 MUTATED RNF32 WILD-TYPE
  0             1              36
  1             4             104
[1] 2 2
[1] FALSE
D47V6, binary
                 cls
clus               0  1
  RNF32 MUTATED    2  0
  RNF32 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF32 MUTATED      2    0
  RNF32 WILD-TYPE   64    4
   clus
vv  RNF32 MUTATED RNF32 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D47V7, binary
                 cls
clus               0  1
  RNF32 MUTATED    1  4
  RNF32 WILD-TYPE 66 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF32 MUTATED      1    4
  RNF32 WILD-TYPE   66   75
        clus
vv       RNF32 MUTATED RNF32 WILD-TYPE
  FEMALE             1              66
  MALE               4              75
[1] 2 2
[1] FALSE
D47V8, binary
                 cls
clus               0  1
  RNF32 MUTATED    4  1
  RNF32 WILD-TYPE 90 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF32 MUTATED      4    1
  RNF32 WILD-TYPE   90   35
     clus
vv    RNF32 MUTATED RNF32 WILD-TYPE
  NO              4              90
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RNF32 MUTATED                                     5
  RNF32 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RNF32 MUTATED                                       0
  RNF32 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RNF32 MUTATED                                                  0
  RNF32 WILD-TYPE                                                2
D47V9, multiclass
                                                  clus
vv                                                 RNF32 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RNF32 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D47V10, continuous
[1] "Remove cluster labels:" "RNF32 MUTATED"         
clus
  RNF32 MUTATED RNF32 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
     TCGA-YY-A8LH 
"RNF32 WILD-TYPE" 
D47V11, continuous
[1] "Remove cluster labels:" "RNF32 MUTATED"         
clus
  RNF32 MUTATED RNF32 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"RNF32 WILD-TYPE" "RNF32 WILD-TYPE" "RNF32 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RNF32 MUTATED    3  2  0  0
  RNF32 WILD-TYPE 76 48  4  3
D47V12, multiclass
    clus
vv   RNF32 MUTATED RNF32 WILD-TYPE
  R0             3              76
  R1             2              48
  R2             0               4
  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"
D47V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF32 MUTATED       0                         0     5
  RNF32 WILD-TYPE     9                         5   123
D47V14, multiclass
                           clus
vv                          RNF32 MUTATED RNF32 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D47V15, binary
                 cls
clus                0   1
  RNF32 MUTATED     1   4
  RNF32 WILD-TYPE   4 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF32 MUTATED      1    4
  RNF32 WILD-TYPE    4  101
                        clus
vv                       RNF32 MUTATED RNF32 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(48) Variable = CBX3 MUTATION ANALYSIS
D48V1, survival
                sevent
clus2             0  1
  CBX3 MUTATED    2  2
  CBX3 WILD-TYPE 66 74
  CBX3 MUTATED CBX3 WILD-TYPE 
             4            140 
  CBX3 MUTATED CBX3 WILD-TYPE 
             2             74 
$`CBX3 MUTATED`
TCGA-2L-AAQI TCGA-FB-AAPU TCGA-H6-8124 TCGA-HV-A5A5 
        3.39        12.53        12.89         9.50 

$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
        4.21         7.63        66.94         8.28        30.25        17.49 
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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CBX3 MUTATED CBX3 WILD-TYPE 
          3.39           0.03 
  CBX3 MUTATED CBX3 WILD-TYPE 
         12.89          75.12 
  CBX3 MUTATED CBX3 WILD-TYPE 
        11.015         14.700 
[1] "3.4 - 12.9 (11.0)" "0.0 - 75.1 (14.7)"
[1] "hr=" "2.2"
D48V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CBX3 MUTATED          0        0         1         3         0        0
  CBX3 WILD-TYPE        3        8        22       100         4        4
D48V3, multiclass
           clus
vv          CBX3 MUTATED CBX3 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            1             22
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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     4
  CBX3 WILD-TYPE   4  16   121
D48V4, multiclass
       clus
vv      CBX3 MUTATED CBX3 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D48V5, binary
                cls
clus               0   1
  CBX3 MUTATED     1   3
  CBX3 WILD-TYPE  36 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      1    3
  CBX3 WILD-TYPE   36  105
   clus
vv  CBX3 MUTATED CBX3 WILD-TYPE
  0            1             36
  1            3            105
[1] 2 2
[1] FALSE
D48V6, binary
                cls
clus              0  1
  CBX3 MUTATED    2  0
  CBX3 WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      2    0
  CBX3 WILD-TYPE   64    4
   clus
vv  CBX3 MUTATED CBX3 WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D48V7, binary
                cls
clus              0  1
  CBX3 MUTATED    3  1
  CBX3 WILD-TYPE 64 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      3    1
  CBX3 WILD-TYPE   64   78
        clus
vv       CBX3 MUTATED CBX3 WILD-TYPE
  FEMALE            3             64
  MALE              1             78
[1] 2 2
[1] FALSE
D48V8, binary
                cls
clus              0  1
  CBX3 MUTATED    3  1
  CBX3 WILD-TYPE 91 35
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      3    1
  CBX3 WILD-TYPE   91   35
     clus
vv    CBX3 MUTATED CBX3 WILD-TYPE
  NO             3             91
  YES            1             35
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CBX3 MUTATED                                     4
  CBX3 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CBX3 MUTATED                                       0
  CBX3 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CBX3 MUTATED                                                  0
  CBX3 WILD-TYPE                                                2
D48V9, multiclass
                                                  clus
vv                                                 CBX3 MUTATED CBX3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D48V10, continuous
[1] "Remove cluster labels:" "CBX3 MUTATED"          
clus
  CBX3 MUTATED CBX3 WILD-TYPE 
             1             49 
    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-HV-AA8V 
"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-7887     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
    TCGA-YY-A8LH 
"CBX3 WILD-TYPE" 
D48V11, continuous
[1] "Remove cluster labels:" "CBX3 MUTATED"          
clus
  CBX3 MUTATED CBX3 WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"CBX3 WILD-TYPE" "CBX3 WILD-TYPE" "CBX3 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CBX3 MUTATED    1  2  0  0
  CBX3 WILD-TYPE 78 48  4  3
D48V12, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  R0            1             78
  R1            2             48
  R2            0              4
  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"
D48V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CBX3 MUTATED       2                         0     2
  CBX3 WILD-TYPE     7                         5   126
D48V14, multiclass
                           clus
vv                          CBX3 MUTATED CBX3 WILD-TYPE
  ASIAN                                2              7
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                2            126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                cls
clus               0   1
  CBX3 MUTATED     0   2
  CBX3 WILD-TYPE   5 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      0    2
  CBX3 WILD-TYPE    5  103
                        clus
vv                       CBX3 MUTATED CBX3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2            103
[1] 2 2
[1] FALSE

Clustering(49) Variable = SDCBP MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2              0  1
  SDCBP MUTATED    2  4
  SDCBP WILD-TYPE 66 72
  SDCBP MUTATED SDCBP WILD-TYPE 
              6             138 
  SDCBP MUTATED SDCBP WILD-TYPE 
              4              72 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       20.19        23.21        12.03        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  SDCBP MUTATED SDCBP WILD-TYPE 
           3.95            0.03 
  SDCBP MUTATED SDCBP WILD-TYPE 
          41.33           75.12 
  SDCBP MUTATED SDCBP WILD-TYPE 
         15.580          14.155 
[1] "4.0 - 41.3 (15.6)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.3"
D49V2, 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        3        8        23        97         4        4
D49V3, multiclass
           clus
vv          SDCBP MUTATED SDCBP WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             6              97
  STAGE III             0               4
  STAGE IV              0               4
[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   3  16   120
D49V4, multiclass
       clus
vv      SDCBP MUTATED SDCBP WILD-TYPE
  T1                1               3
  T2                0              16
  T3+T4             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"
D49V5, binary
                 cls
clus                0   1
  SDCBP MUTATED     0   6
  SDCBP WILD-TYPE  37 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDCBP MUTATED      0    6
  SDCBP WILD-TYPE   37  102
   clus
vv  SDCBP MUTATED SDCBP WILD-TYPE
  0             0              37
  1             6             102
[1] 2 2
[1] FALSE
D49V6, binary
                 cls
clus               0  1
  SDCBP MUTATED    3  0
  SDCBP WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDCBP MUTATED      3    0
  SDCBP WILD-TYPE   63    4
   clus
vv  SDCBP MUTATED SDCBP WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D49V7, binary
                 cls
clus               0  1
  SDCBP MUTATED    3  3
  SDCBP WILD-TYPE 64 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDCBP MUTATED      3    3
  SDCBP WILD-TYPE   64   76
        clus
vv       SDCBP MUTATED SDCBP WILD-TYPE
  FEMALE             3              64
  MALE               3              76
[1] 2 2
[1] FALSE
D49V8, binary
                 cls
clus               0  1
  SDCBP MUTATED    4  1
  SDCBP WILD-TYPE 90 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDCBP MUTATED      4    1
  SDCBP WILD-TYPE   90   35
     clus
vv    SDCBP MUTATED SDCBP WILD-TYPE
  NO              4              90
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SDCBP MUTATED                                     6
  SDCBP WILD-TYPE                                 124
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SDCBP MUTATED                                       0
  SDCBP WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SDCBP MUTATED                                                  0
  SDCBP WILD-TYPE                                                2
D49V9, 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                          124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D49V10, continuous
[1] "Remove cluster labels:" "SDCBP MUTATED"         
clus
  SDCBP MUTATED SDCBP WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
D49V11, continuous
[1] "Remove cluster labels:" "SDCBP MUTATED"         
clus
  SDCBP MUTATED SDCBP WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"SDCBP WILD-TYPE" "SDCBP WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SDCBP MUTATED    3  2  0  1
  SDCBP WILD-TYPE 76 48  4  2
D49V12, multiclass
    clus
vv   SDCBP MUTATED SDCBP WILD-TYPE
  R0             3              76
  R1             2              48
  R2             0               4
  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"
D49V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SDCBP MUTATED       0                         1     4
  SDCBP WILD-TYPE     9                         4   124
D49V14, multiclass
                           clus
vv                          SDCBP MUTATED SDCBP WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                 cls
clus                0   1
  SDCBP MUTATED     0   5
  SDCBP WILD-TYPE   5 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDCBP MUTATED      0    5
  SDCBP WILD-TYPE    5  100
                        clus
vv                       SDCBP MUTATED SDCBP WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             100
[1] 2 2
[1] FALSE

Clustering(50) Variable = PLIN4 MUTATION ANALYSIS
D50V1, survival
                 sevent
clus2              0  1
  PLIN4 MUTATED    2  5
  PLIN4 WILD-TYPE 66 71
  PLIN4 MUTATED PLIN4 WILD-TYPE 
              7             137 
  PLIN4 MUTATED PLIN4 WILD-TYPE 
              5              71 
$`PLIN4 MUTATED`
TCGA-FB-AAPY TCGA-HV-A5A4 TCGA-HZ-7926 TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-A5SQ 
       34.82         7.63        17.03        12.95        19.82         7.20 
TCGA-RB-AA9M 
        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       12.89        13.84         4.21         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7645 
        5.26        10.85         1.08         0.23        19.82        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-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-S4-A8RM 
        8.78        15.45        13.68         3.12        15.32        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
        0.39        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  PLIN4 MUTATED PLIN4 WILD-TYPE 
           7.20            0.03 
  PLIN4 MUTATED PLIN4 WILD-TYPE 
          34.82           75.12 
  PLIN4 MUTATED PLIN4 WILD-TYPE 
          12.95           14.40 
[1] "7.2 - 34.8 (12.9)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.5"
D50V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PLIN4 MUTATED          0        1         1         4         0        1
  PLIN4 WILD-TYPE        3        7        22        99         4        3
D50V3, multiclass
           clus
vv          PLIN4 MUTATED PLIN4 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             1              22
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              1               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
  PLIN4 MUTATED     1   2     4
  PLIN4 WILD-TYPE   3  14   121
D50V4, multiclass
       clus
vv      PLIN4 MUTATED PLIN4 WILD-TYPE
  T1                1               3
  T2                2              14
  T3+T4             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"
D50V5, binary
                 cls
clus                0   1
  PLIN4 MUTATED     2   5
  PLIN4 WILD-TYPE  35 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN4 MUTATED      2    5
  PLIN4 WILD-TYPE   35  103
   clus
vv  PLIN4 MUTATED PLIN4 WILD-TYPE
  0             2              35
  1             5             103
[1] 2 2
[1] FALSE
D50V6, binary
                 cls
clus               0  1
  PLIN4 MUTATED    2  1
  PLIN4 WILD-TYPE 64  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN4 MUTATED      2    1
  PLIN4 WILD-TYPE   64    3
   clus
vv  PLIN4 MUTATED PLIN4 WILD-TYPE
  0             2              64
  1             1               3
[1] 2 2
[1] FALSE
D50V7, binary
                 cls
clus               0  1
  PLIN4 MUTATED    4  3
  PLIN4 WILD-TYPE 63 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN4 MUTATED      4    3
  PLIN4 WILD-TYPE   63   76
        clus
vv       PLIN4 MUTATED PLIN4 WILD-TYPE
  FEMALE             4              63
  MALE               3              76
[1] 2 2
[1] FALSE
D50V8, binary
                 cls
clus               0  1
  PLIN4 MUTATED    4  2
  PLIN4 WILD-TYPE 90 34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN4 MUTATED      4    2
  PLIN4 WILD-TYPE   90   34
     clus
vv    PLIN4 MUTATED PLIN4 WILD-TYPE
  NO              4              90
  YES             2              34
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PLIN4 MUTATED                                     7
  PLIN4 WILD-TYPE                                 123
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PLIN4 MUTATED                                       0
  PLIN4 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PLIN4 MUTATED                                                  0
  PLIN4 WILD-TYPE                                                2
D50V9, multiclass
                                                  clus
vv                                                 PLIN4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PLIN4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D50V10, continuous
D50V11, continuous
                 vv
clus              R0 R1 R2 RX
  PLIN4 MUTATED    4  1  0  1
  PLIN4 WILD-TYPE 75 49  4  2
D50V12, multiclass
    clus
vv   PLIN4 MUTATED PLIN4 WILD-TYPE
  R0             4              75
  R1             1              49
  R2             0               4
  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"
D50V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLIN4 MUTATED       1                         1     5
  PLIN4 WILD-TYPE     8                         4   123
D50V14, multiclass
                           clus
vv                          PLIN4 MUTATED PLIN4 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             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"
D50V15, binary
                 cls
clus               0  1
  PLIN4 MUTATED    0  6
  PLIN4 WILD-TYPE  5 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLIN4 MUTATED      0    6
  PLIN4 WILD-TYPE    5   99
                        clus
vv                       PLIN4 MUTATED PLIN4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              99
[1] 2 2
[1] FALSE

Clustering(51) Variable = AAK1 MUTATION ANALYSIS
D51V1, survival
                sevent
clus2             0  1
  AAK1 MUTATED    0  4
  AAK1 WILD-TYPE 68 72
  AAK1 MUTATED AAK1 WILD-TYPE 
             4            140 
  AAK1 MUTATED AAK1 WILD-TYPE 
             4             72 
$`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        42.31        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        58.98        43.50        20.84        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       19.82        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
       15.81        21.30         3.85         2.47        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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  AAK1 MUTATED AAK1 WILD-TYPE 
          7.20           0.03 
  AAK1 MUTATED AAK1 WILD-TYPE 
         19.66          75.12 
  AAK1 MUTATED AAK1 WILD-TYPE 
        11.670         14.285 
[1] "7.2 - 19.7 (11.7)" "0.0 - 75.1 (14.3)"
[1] "hr=" "2.7"
D51V2, 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        3        6        23       101         4        4
D51V3, multiclass
           clus
vv          AAK1 MUTATED AAK1 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             2              6
  STAGE IIA            0             23
  STAGE IIB            2            101
  STAGE III            0              4
  STAGE IV             0              4
[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   4  14   123
D51V4, multiclass
       clus
vv      AAK1 MUTATED AAK1 WILD-TYPE
  T1               0              4
  T2               2             14
  T3+T4            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"
D51V5, binary
                cls
clus               0   1
  AAK1 MUTATED     2   2
  AAK1 WILD-TYPE  35 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAK1 MUTATED      2    2
  AAK1 WILD-TYPE   35  106
   clus
vv  AAK1 MUTATED AAK1 WILD-TYPE
  0            2             35
  1            2            106
[1] 2 2
[1] FALSE
D51V6, binary
                cls
clus              0  1
  AAK1 MUTATED    3  0
  AAK1 WILD-TYPE 63  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAK1 MUTATED      3    0
  AAK1 WILD-TYPE   63    4
   clus
vv  AAK1 MUTATED AAK1 WILD-TYPE
  0            3             63
  1            0              4
[1] 2 2
[1] FALSE
D51V7, binary
                cls
clus              0  1
  AAK1 MUTATED    3  1
  AAK1 WILD-TYPE 64 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAK1 MUTATED      3    1
  AAK1 WILD-TYPE   64   78
        clus
vv       AAK1 MUTATED AAK1 WILD-TYPE
  FEMALE            3             64
  MALE              1             78
[1] 2 2
[1] FALSE
D51V8, binary
                cls
clus              0  1
  AAK1 MUTATED    4  0
  AAK1 WILD-TYPE 90 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAK1 MUTATED      4    0
  AAK1 WILD-TYPE   90   36
     clus
vv    AAK1 MUTATED AAK1 WILD-TYPE
  NO             4             90
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AAK1 MUTATED                                     4
  AAK1 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AAK1 MUTATED                                       0
  AAK1 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AAK1 MUTATED                                                  0
  AAK1 WILD-TYPE                                                2
D51V9, multiclass
                                                  clus
vv                                                 AAK1 MUTATED AAK1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D51V10, continuous
[1] "Remove cluster labels:" "AAK1 MUTATED"          
clus
  AAK1 MUTATED AAK1 WILD-TYPE 
             1             49 
    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-HV-AA8V 
"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-7887     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
    TCGA-YY-A8LH 
"AAK1 WILD-TYPE" 
D51V11, continuous
[1] "Remove cluster labels:" "AAK1 MUTATED"          
clus
  AAK1 MUTATED AAK1 WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"AAK1 WILD-TYPE" "AAK1 WILD-TYPE" "AAK1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  AAK1 MUTATED    4  0  0  0
  AAK1 WILD-TYPE 75 50  4  3
D51V12, multiclass
    clus
vv   AAK1 MUTATED AAK1 WILD-TYPE
  R0            4             75
  R1            0             50
  R2            0              4
  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"
D51V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AAK1 MUTATED       0                         0     3
  AAK1 WILD-TYPE     9                         5   125
D51V14, multiclass
                           clus
vv                          AAK1 MUTATED AAK1 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                cls
clus               0   1
  AAK1 MUTATED     0   3
  AAK1 WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAK1 MUTATED      0    3
  AAK1 WILD-TYPE    5  102
                        clus
vv                       AAK1 MUTATED AAK1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(52) Variable = TMCC1 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2              0  1
  TMCC1 MUTATED    2  5
  TMCC1 WILD-TYPE 66 71
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              7             137 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              5              71 
$`TMCC1 MUTATED`
TCGA-2J-AABV TCGA-3A-A9I7 TCGA-3A-A9IB TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7651 
       21.44        43.50         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        42.31        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 
       58.98        20.84        24.26        33.57        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        24.43        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-A77P TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 
       10.85         0.23        19.82        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-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 
       43.79        15.81        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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
        0.39        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  TMCC1 MUTATED TMCC1 WILD-TYPE 
           1.08            0.03 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
          43.50           75.12 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
          19.66           14.17 
[1] "1.1 - 43.5 (19.7)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.4"
D52V2, 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        3        7        23        97         4        4
D52V3, multiclass
           clus
vv          TMCC1 MUTATED TMCC1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             0              23
  STAGE IIB             6              97
  STAGE III             0               4
  STAGE IV              0               4
[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   4  14   120
D52V4, multiclass
       clus
vv      TMCC1 MUTATED TMCC1 WILD-TYPE
  T1                0               4
  T2                2              14
  T3+T4             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"
D52V5, binary
                 cls
clus                0   1
  TMCC1 MUTATED     1   6
  TMCC1 WILD-TYPE  36 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      1    6
  TMCC1 WILD-TYPE   36  102
   clus
vv  TMCC1 MUTATED TMCC1 WILD-TYPE
  0             1              36
  1             6             102
[1] 2 2
[1] FALSE
D52V6, binary
                 cls
clus               0  1
  TMCC1 MUTATED    3  0
  TMCC1 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      3    0
  TMCC1 WILD-TYPE   63    4
   clus
vv  TMCC1 MUTATED TMCC1 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D52V7, binary
                 cls
clus               0  1
  TMCC1 MUTATED    4  3
  TMCC1 WILD-TYPE 63 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      4    3
  TMCC1 WILD-TYPE   63   76
        clus
vv       TMCC1 MUTATED TMCC1 WILD-TYPE
  FEMALE             4              63
  MALE               3              76
[1] 2 2
[1] FALSE
D52V8, binary
                 cls
clus               0  1
  TMCC1 MUTATED    5  1
  TMCC1 WILD-TYPE 89 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      5    1
  TMCC1 WILD-TYPE   89   35
     clus
vv    TMCC1 MUTATED TMCC1 WILD-TYPE
  NO              5              89
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMCC1 MUTATED                                     6
  TMCC1 WILD-TYPE                                 124
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMCC1 MUTATED                                       1
  TMCC1 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMCC1 MUTATED                                                  0
  TMCC1 WILD-TYPE                                                2
D52V9, 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                          124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D52V10, continuous
D52V11, continuous
                 vv
clus              R0 R1 R2 RX
  TMCC1 MUTATED    6  1  0  0
  TMCC1 WILD-TYPE 73 49  4  3
D52V12, multiclass
    clus
vv   TMCC1 MUTATED TMCC1 WILD-TYPE
  R0             6              73
  R1             1              49
  R2             0               4
  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"
D52V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMCC1 MUTATED       0                         1     5
  TMCC1 WILD-TYPE     9                         4   123
D52V14, multiclass
                           clus
vv                          TMCC1 MUTATED TMCC1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             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"
D52V15, binary
                 cls
clus                0   1
  TMCC1 MUTATED     0   5
  TMCC1 WILD-TYPE   5 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      0    5
  TMCC1 WILD-TYPE    5  100
                        clus
vv                       TMCC1 MUTATED TMCC1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             100
[1] 2 2
[1] FALSE

Clustering(53) Variable = IYD MUTATION ANALYSIS
D53V1, survival
               sevent
clus2            0  1
  IYD MUTATED    3  3
  IYD WILD-TYPE 65 73
  IYD MUTATED IYD WILD-TYPE 
            6           138 
  IYD MUTATED IYD WILD-TYPE 
            3            73 
$`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        15.35 

$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        14.14         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 

  IYD MUTATED IYD WILD-TYPE 
        10.13          0.03 
  IYD MUTATED IYD WILD-TYPE 
        23.54         75.12 
  IYD MUTATED IYD WILD-TYPE 
       15.450        14.155 
[1] "10.1 - 23.5 (15.4)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "1.1"
D53V2, 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        3        8        20       100         4        4
D53V3, multiclass
           clus
vv          IYD MUTATED IYD WILD-TYPE
  STAGE IA            0             3
  STAGE IB            0             8
  STAGE IIA           3            20
  STAGE IIB           3           100
  STAGE III           0             4
  STAGE IV            0             4
[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   4  15   120
D53V4, multiclass
       clus
vv      IYD MUTATED IYD WILD-TYPE
  T1              0             4
  T2              1            15
  T3+T4           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"
D53V5, binary
               cls
clus              0   1
  IYD MUTATED     3   3
  IYD WILD-TYPE  34 105
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      3    3
  IYD WILD-TYPE   34  105
   clus
vv  IYD MUTATED IYD WILD-TYPE
  0           3            34
  1           3           105
[1] 2 2
[1] FALSE
D53V6, binary
               cls
clus             0  1
  IYD MUTATED    1  0
  IYD WILD-TYPE 65  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      1    0
  IYD WILD-TYPE   65    4
   clus
vv  IYD MUTATED IYD WILD-TYPE
  0           1            65
  1           0             4
[1] 2 2
[1] FALSE
D53V7, binary
               cls
clus             0  1
  IYD MUTATED    3  3
  IYD WILD-TYPE 64 76
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      3    3
  IYD WILD-TYPE   64   76
        clus
vv       IYD MUTATED IYD WILD-TYPE
  FEMALE           3            64
  MALE             3            76
[1] 2 2
[1] FALSE
D53V8, binary
               cls
clus             0  1
  IYD MUTATED    3  2
  IYD WILD-TYPE 91 34
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      3    2
  IYD WILD-TYPE   91   34
     clus
vv    IYD MUTATED IYD WILD-TYPE
  NO            3            91
  YES           2            34
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IYD MUTATED                                     6
  IYD WILD-TYPE                                 124
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IYD MUTATED                                       0
  IYD WILD-TYPE                                    13
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IYD MUTATED                                                  0
  IYD WILD-TYPE                                                2
D53V9, multiclass
                                                  clus
vv                                                 IYD MUTATED IYD WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        6           124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            13
  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"
D53V10, continuous
D53V11, continuous
               vv
clus            R0 R1 R2 RX
  IYD MUTATED    5  1  0  0
  IYD WILD-TYPE 74 49  4  3
D53V12, multiclass
    clus
vv   IYD MUTATED IYD WILD-TYPE
  R0           5            74
  R1           1            49
  R2           0             4
  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"
D53V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IYD MUTATED       0                         1     5
  IYD WILD-TYPE     9                         4   123
D53V14, multiclass
                           clus
vv                          IYD MUTATED IYD WILD-TYPE
  ASIAN                               0             9
  BLACK OR AFRICAN AMERICAN           1             4
  WHITE                               5           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"
D53V15, binary
               cls
clus             0  1
  IYD MUTATED    0  6
  IYD WILD-TYPE  5 99
[1] "tbl2"
               cls
clus            [,1] [,2]
  IYD MUTATED      0    6
  IYD WILD-TYPE    5   99
                        clus
vv                       IYD MUTATED IYD WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           6            99
[1] 2 2
[1] FALSE

Clustering(54) Variable = NLRP2 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2              0  1
  NLRP2 MUTATED    2  4
  NLRP2 WILD-TYPE 66 72
  NLRP2 MUTATED NLRP2 WILD-TYPE 
              6             138 
  NLRP2 MUTATED NLRP2 WILD-TYPE 
              4              72 
$`NLRP2 MUTATED`
TCGA-F2-A44G TCGA-HZ-A49I TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-8127 TCGA-OE-A75W 
        7.66        10.13        19.82        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
       12.43        14.93        17.92        21.70        16.14         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-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-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 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  NLRP2 MUTATED NLRP2 WILD-TYPE 
           7.66            0.03 
  NLRP2 MUTATED NLRP2 WILD-TYPE 
          19.82           75.12 
  NLRP2 MUTATED NLRP2 WILD-TYPE 
         13.645          14.285 
[1] "7.7 - 19.8 (13.6)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.5"
D54V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NLRP2 MUTATED          0        0         1         4         0        1
  NLRP2 WILD-TYPE        3        8        22        99         4        3
D54V3, multiclass
           clus
vv          NLRP2 MUTATED NLRP2 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              1               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     6
  NLRP2 WILD-TYPE   4  16   119
D54V4, multiclass
       clus
vv      NLRP2 MUTATED NLRP2 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D54V5, binary
                 cls
clus                0   1
  NLRP2 MUTATED     2   4
  NLRP2 WILD-TYPE  35 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP2 MUTATED      2    4
  NLRP2 WILD-TYPE   35  104
   clus
vv  NLRP2 MUTATED NLRP2 WILD-TYPE
  0             2              35
  1             4             104
[1] 2 2
[1] FALSE
D54V6, binary
                 cls
clus               0  1
  NLRP2 MUTATED    4  1
  NLRP2 WILD-TYPE 62  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP2 MUTATED      4    1
  NLRP2 WILD-TYPE   62    3
   clus
vv  NLRP2 MUTATED NLRP2 WILD-TYPE
  0             4              62
  1             1               3
[1] 2 2
[1] FALSE
D54V7, binary
                 cls
clus               0  1
  NLRP2 MUTATED    2  4
  NLRP2 WILD-TYPE 65 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP2 MUTATED      2    4
  NLRP2 WILD-TYPE   65   75
        clus
vv       NLRP2 MUTATED NLRP2 WILD-TYPE
  FEMALE             2              65
  MALE               4              75
[1] 2 2
[1] FALSE
D54V8, binary
                 cls
clus               0  1
  NLRP2 MUTATED    3  3
  NLRP2 WILD-TYPE 91 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP2 MUTATED      3    3
  NLRP2 WILD-TYPE   91   33
     clus
vv    NLRP2 MUTATED NLRP2 WILD-TYPE
  NO              3              91
  YES             3              33
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NLRP2 MUTATED                                     5
  NLRP2 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NLRP2 MUTATED                                       1
  NLRP2 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NLRP2 MUTATED                                                  0
  NLRP2 WILD-TYPE                                                2
D54V9, multiclass
                                                  clus
vv                                                 NLRP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NLRP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D54V10, continuous
D54V11, continuous
                 vv
clus              R0 R1 R2 RX
  NLRP2 MUTATED    3  3  0  0
  NLRP2 WILD-TYPE 76 47  4  3
D54V12, multiclass
    clus
vv   NLRP2 MUTATED NLRP2 WILD-TYPE
  R0             3              76
  R1             3              47
  R2             0               4
  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"
D54V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLRP2 MUTATED       0                         0     6
  NLRP2 WILD-TYPE     9                         5   122
D54V14, multiclass
                           clus
vv                          NLRP2 MUTATED NLRP2 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             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"
D54V15, binary
                 cls
clus               0  1
  NLRP2 MUTATED    0  6
  NLRP2 WILD-TYPE  5 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP2 MUTATED      0    6
  NLRP2 WILD-TYPE    5   99
                        clus
vv                       NLRP2 MUTATED NLRP2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              99
[1] 2 2
[1] FALSE

Clustering(55) Variable = SP140 MUTATION ANALYSIS
D55V1, survival
                 sevent
clus2              0  1
  SP140 MUTATED    0  4
  SP140 WILD-TYPE 68 72
  SP140 MUTATED SP140 WILD-TYPE 
              4             140 
  SP140 MUTATED SP140 WILD-TYPE 
              4              72 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SP140 MUTATED SP140 WILD-TYPE 
           9.63            0.03 
  SP140 MUTATED SP140 WILD-TYPE 
          20.19           75.12 
  SP140 MUTATED SP140 WILD-TYPE 
         17.470          14.155 
[1] "9.6 - 20.2 (17.5)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.9"
D55V2, 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        3        8        22        99         4        4
D55V3, multiclass
           clus
vv          SP140 MUTATED SP140 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   120
D55V4, multiclass
       clus
vv      SP140 MUTATED SP140 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D55V5, binary
                 cls
clus                0   1
  SP140 MUTATED     1   4
  SP140 WILD-TYPE  36 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      1    4
  SP140 WILD-TYPE   36  104
   clus
vv  SP140 MUTATED SP140 WILD-TYPE
  0             1              36
  1             4             104
[1] 2 2
[1] FALSE
D55V6, binary
                 cls
clus               0  1
  SP140 MUTATED    3  0
  SP140 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      3    0
  SP140 WILD-TYPE   63    4
   clus
vv  SP140 MUTATED SP140 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D55V7, binary
                 cls
clus               0  1
  SP140 MUTATED    2  3
  SP140 WILD-TYPE 65 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      2    3
  SP140 WILD-TYPE   65   76
        clus
vv       SP140 MUTATED SP140 WILD-TYPE
  FEMALE             2              65
  MALE               3              76
[1] 2 2
[1] FALSE
D55V8, binary
                 cls
clus               0  1
  SP140 MUTATED    4  0
  SP140 WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      4    0
  SP140 WILD-TYPE   90   36
     clus
vv    SP140 MUTATED SP140 WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SP140 MUTATED                                     5
  SP140 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SP140 MUTATED                                       0
  SP140 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SP140 MUTATED                                                  0
  SP140 WILD-TYPE                                                2
D55V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D55V10, continuous
D55V11, continuous
                 vv
clus              R0 R1 R2 RX
  SP140 MUTATED    5  0  0  0
  SP140 WILD-TYPE 74 50  4  3
D55V12, multiclass
    clus
vv   SP140 MUTATED SP140 WILD-TYPE
  R0             5              74
  R1             0              50
  R2             0               4
  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"
D55V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SP140 MUTATED       0                         0     5
  SP140 WILD-TYPE     9                         5   123
D55V14, multiclass
                           clus
vv                          SP140 MUTATED SP140 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D55V15, binary
                 cls
clus                0   1
  SP140 MUTATED     0   4
  SP140 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP140 MUTATED      0    4
  SP140 WILD-TYPE    5  101
                        clus
vv                       SP140 MUTATED SP140 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(56) Variable = OR2T4 MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2              0  1
  OR2T4 MUTATED    2  4
  OR2T4 WILD-TYPE 66 72
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              6             138 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              4              72 
$`OR2T4 MUTATED`
TCGA-HV-A5A3 TCGA-HV-A5A6 TCGA-HZ-8003 TCGA-HZ-A49H TCGA-IB-7651 TCGA-US-A776 
        4.21        66.94        19.59        16.14        19.82        39.98 

$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A7OL 
        1.02        12.89        13.84         7.63         9.50         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        19.50         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-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-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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        24.23        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  OR2T4 MUTATED OR2T4 WILD-TYPE 
           4.21            0.03 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
          66.94           75.12 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
         19.705          13.990 
[1] "4.2 - 66.9 (19.7)" "0.0 - 75.1 (14.0)"
[1] "hr=" "1.3"
D56V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OR2T4 MUTATED          0        0         2         4         0        0
  OR2T4 WILD-TYPE        3        8        21        99         4        4
D56V3, multiclass
           clus
vv          OR2T4 MUTATED OR2T4 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             2              21
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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     6
  OR2T4 WILD-TYPE   4  16   119
D56V4, multiclass
       clus
vv      OR2T4 MUTATED OR2T4 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D56V5, binary
                 cls
clus                0   1
  OR2T4 MUTATED     1   4
  OR2T4 WILD-TYPE  36 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      1    4
  OR2T4 WILD-TYPE   36  104
   clus
vv  OR2T4 MUTATED OR2T4 WILD-TYPE
  0             1              36
  1             4             104
[1] 2 2
[1] FALSE
D56V6, binary
                 cls
clus               0  1
  OR2T4 MUTATED    2  0
  OR2T4 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      2    0
  OR2T4 WILD-TYPE   64    4
   clus
vv  OR2T4 MUTATED OR2T4 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D56V7, binary
                 cls
clus               0  1
  OR2T4 MUTATED    4  2
  OR2T4 WILD-TYPE 63 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      4    2
  OR2T4 WILD-TYPE   63   77
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  FEMALE             4              63
  MALE               2              77
[1] 2 2
[1] FALSE
D56V8, binary
                 cls
clus               0  1
  OR2T4 MUTATED    6  0
  OR2T4 WILD-TYPE 88 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      6    0
  OR2T4 WILD-TYPE   88   36
     clus
vv    OR2T4 MUTATED OR2T4 WILD-TYPE
  NO              6              88
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR2T4 MUTATED                                     5
  OR2T4 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR2T4 MUTATED                                       0
  OR2T4 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR2T4 MUTATED                                                  1
  OR2T4 WILD-TYPE                                                1
D56V9, multiclass
                                                  clus
vv                                                 OR2T4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 OR2T4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D56V10, continuous
[1] "Remove cluster labels:" "OR2T4 MUTATED"         
clus
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
     TCGA-YY-A8LH 
"OR2T4 WILD-TYPE" 
D56V11, continuous
[1] "Remove cluster labels:" "OR2T4 MUTATED"         
clus
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" "OR2T4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  OR2T4 MUTATED    5  0  0  0
  OR2T4 WILD-TYPE 74 50  4  3
D56V12, multiclass
    clus
vv   OR2T4 MUTATED OR2T4 WILD-TYPE
  R0             5              74
  R1             0              50
  R2             0               4
  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"
D56V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR2T4 MUTATED       2                         0     4
  OR2T4 WILD-TYPE     7                         5   124
D56V14, multiclass
                           clus
vv                          OR2T4 MUTATED OR2T4 WILD-TYPE
  ASIAN                                 2               7
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                 cls
clus                0   1
  OR2T4 MUTATED     0   4
  OR2T4 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      0    4
  OR2T4 WILD-TYPE    5  101
                        clus
vv                       OR2T4 MUTATED OR2T4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(57) Variable = GPR50 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2              0  1
  GPR50 MUTATED    2  3
  GPR50 WILD-TYPE 66 73
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             139 
  GPR50 MUTATED GPR50 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        19.50         0.13        20.19 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
       17.03        12.03        19.59         9.83        12.43        14.93 
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-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  GPR50 MUTATED GPR50 WILD-TYPE 
           3.85            0.03 
  GPR50 MUTATED GPR50 WILD-TYPE 
          23.21           75.12 
  GPR50 MUTATED GPR50 WILD-TYPE 
          16.14           14.17 
[1] "3.9 - 23.2 (16.1)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.2"
D57V2, 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        3        8        21       101         3        4
D57V3, multiclass
           clus
vv          GPR50 MUTATED GPR50 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             2              21
  STAGE IIB             2             101
  STAGE III             1               3
  STAGE IV              0               4
[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   4  16   120
D57V4, multiclass
       clus
vv      GPR50 MUTATED GPR50 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D57V5, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   2
  GPR50 WILD-TYPE  34 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    2
  GPR50 WILD-TYPE   34  106
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             3              34
  1             2             106
[1] 2 2
[1] FALSE
D57V6, binary
                 cls
clus               0  1
  GPR50 MUTATED    1  0
  GPR50 WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      1    0
  GPR50 WILD-TYPE   65    4
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D57V7, binary
                 cls
clus               0  1
  GPR50 MUTATED    1  4
  GPR50 WILD-TYPE 66 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      1    4
  GPR50 WILD-TYPE   66   75
        clus
vv       GPR50 MUTATED GPR50 WILD-TYPE
  FEMALE             1              66
  MALE               4              75
[1] 2 2
[1] FALSE
D57V8, binary
                 cls
clus               0  1
  GPR50 MUTATED    4  1
  GPR50 WILD-TYPE 90 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      4    1
  GPR50 WILD-TYPE   90   35
     clus
vv    GPR50 MUTATED GPR50 WILD-TYPE
  NO              4              90
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPR50 MUTATED                                     5
  GPR50 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPR50 MUTATED                                       0
  GPR50 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPR50 MUTATED                                                  0
  GPR50 WILD-TYPE                                                2
D57V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D57V10, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1              49 
     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-HV-AA8V 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-YY-A8LH 
"GPR50 WILD-TYPE" 
D57V11, continuous
                 vv
clus              R0 R1 R2 RX
  GPR50 MUTATED    4  1  0  0
  GPR50 WILD-TYPE 75 49  4  3
D57V12, multiclass
    clus
vv   GPR50 MUTATED GPR50 WILD-TYPE
  R0             4              75
  R1             1              49
  R2             0               4
  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"
D57V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR50 MUTATED       0                         0     5
  GPR50 WILD-TYPE     9                         5   123
D57V14, multiclass
                           clus
vv                          GPR50 MUTATED GPR50 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D57V15, binary
                 cls
clus                0   1
  GPR50 MUTATED     0   5
  GPR50 WILD-TYPE   5 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      0    5
  GPR50 WILD-TYPE    5  100
                        clus
vv                       GPR50 MUTATED GPR50 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             100
[1] 2 2
[1] FALSE

Clustering(58) Variable = CFTR MUTATION ANALYSIS
D58V1, survival
                sevent
clus2             0  1
  CFTR MUTATED    2  5
  CFTR WILD-TYPE 66 71
  CFTR MUTATED CFTR WILD-TYPE 
             7            137 
  CFTR MUTATED CFTR WILD-TYPE 
             5             71 
$`CFTR MUTATED`
TCGA-3A-A9I5 TCGA-3E-AAAZ TCGA-HZ-8317 TCGA-IB-7651 TCGA-IB-7888 TCGA-IB-7893 
       58.98        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        42.31        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        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-7897 
        4.04         3.62        15.81        19.66        21.30        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 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        12.76        66.28        15.35 

  CFTR MUTATED CFTR WILD-TYPE 
          3.85           0.03 
  CFTR MUTATED CFTR WILD-TYPE 
         71.74          75.12 
  CFTR MUTATED CFTR WILD-TYPE 
         19.82          14.17 
[1] "3.9 - 71.7 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.4"
D58V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CFTR MUTATED          0        0         3         3         0        0
  CFTR WILD-TYPE        3        8        20       100         4        4
D58V3, multiclass
           clus
vv          CFTR MUTATED CFTR WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            3             20
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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     0   0     6
  CFTR WILD-TYPE   4  16   119
D58V4, multiclass
       clus
vv      CFTR MUTATED CFTR WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D58V5, binary
                cls
clus               0   1
  CFTR MUTATED     4   3
  CFTR WILD-TYPE  33 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  CFTR MUTATED      4    3
  CFTR WILD-TYPE   33  105
   clus
vv  CFTR MUTATED CFTR WILD-TYPE
  0            4             33
  1            3            105
[1] 2 2
[1] FALSE
D58V6, binary
                cls
clus              0  1
  CFTR MUTATED    3  0
  CFTR WILD-TYPE 63  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CFTR MUTATED      3    0
  CFTR WILD-TYPE   63    4
   clus
vv  CFTR MUTATED CFTR WILD-TYPE
  0            3             63
  1            0              4
[1] 2 2
[1] FALSE
D58V7, binary
                cls
clus              0  1
  CFTR MUTATED    3  4
  CFTR WILD-TYPE 64 75
[1] "tbl2"
                cls
clus             [,1] [,2]
  CFTR MUTATED      3    4
  CFTR WILD-TYPE   64   75
        clus
vv       CFTR MUTATED CFTR WILD-TYPE
  FEMALE            3             64
  MALE              4             75
[1] 2 2
[1] FALSE
D58V8, binary
                cls
clus              0  1
  CFTR MUTATED    3  3
  CFTR WILD-TYPE 91 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  CFTR MUTATED      3    3
  CFTR WILD-TYPE   91   33
     clus
vv    CFTR MUTATED CFTR WILD-TYPE
  NO             3             91
  YES            3             33
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CFTR MUTATED                                     7
  CFTR WILD-TYPE                                 123
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CFTR MUTATED                                       0
  CFTR WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CFTR MUTATED                                                  0
  CFTR WILD-TYPE                                                2
D58V9, multiclass
                                                  clus
vv                                                 CFTR MUTATED CFTR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         7            123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D58V10, continuous
[1] "Remove cluster labels:" "CFTR MUTATED"          
clus
  CFTR MUTATED CFTR WILD-TYPE 
             1             49 
    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-HV-AA8V     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-7887     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
    TCGA-YY-A8LH 
"CFTR WILD-TYPE" 
D58V11, continuous
[1] "Remove cluster labels:" "CFTR MUTATED"          
clus
  CFTR MUTATED CFTR WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"CFTR WILD-TYPE" "CFTR WILD-TYPE" "CFTR WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  CFTR MUTATED    5  1  0  0
  CFTR WILD-TYPE 74 49  4  3
D58V12, multiclass
    clus
vv   CFTR MUTATED CFTR WILD-TYPE
  R0            5             74
  R1            1             49
  R2            0              4
  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"
D58V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CFTR MUTATED       0                         1     6
  CFTR WILD-TYPE     9                         4   122
D58V14, multiclass
                           clus
vv                          CFTR MUTATED CFTR WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                6            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"
D58V15, binary
                cls
clus              0  1
  CFTR MUTATED    1  6
  CFTR WILD-TYPE  4 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  CFTR MUTATED      1    6
  CFTR WILD-TYPE    4   99
                        clus
vv                       CFTR MUTATED CFTR WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            6             99
[1] 2 2
[1] FALSE

Clustering(59) Variable = GPR98 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2              0  1
  GPR98 MUTATED    3  5
  GPR98 WILD-TYPE 65 71
  GPR98 MUTATED GPR98 WILD-TYPE 
              8             136 
  GPR98 MUTATED GPR98 WILD-TYPE 
              5              71 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       33.57        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8002 
        8.28        30.25        17.49        19.50         0.13        12.03 
TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  GPR98 MUTATED GPR98 WILD-TYPE 
          12.46            0.03 
  GPR98 MUTATED GPR98 WILD-TYPE 
          41.33           75.12 
  GPR98 MUTATED GPR98 WILD-TYPE 
         18.425          13.825 
[1] "12.5 - 41.3 (18.4)" "0.0 - 75.1 (13.8)" 
[1] "hr=" "1.1"
D59V2, 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        3        8        22        97         3        4
D59V3, multiclass
           clus
vv          GPR98 MUTATED GPR98 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             6              97
  STAGE III             1               3
  STAGE IV              0               4
[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   4  16   117
D59V4, multiclass
       clus
vv      GPR98 MUTATED GPR98 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D59V5, binary
                 cls
clus                0   1
  GPR98 MUTATED     2   6
  GPR98 WILD-TYPE  35 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED      2    6
  GPR98 WILD-TYPE   35  102
   clus
vv  GPR98 MUTATED GPR98 WILD-TYPE
  0             2              35
  1             6             102
[1] 2 2
[1] FALSE
D59V6, binary
                 cls
clus               0  1
  GPR98 MUTATED    3  0
  GPR98 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED      3    0
  GPR98 WILD-TYPE   63    4
   clus
vv  GPR98 MUTATED GPR98 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D59V7, binary
                 cls
clus               0  1
  GPR98 MUTATED    4  4
  GPR98 WILD-TYPE 63 75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED      4    4
  GPR98 WILD-TYPE   63   75
        clus
vv       GPR98 MUTATED GPR98 WILD-TYPE
  FEMALE             4              63
  MALE               4              75
[1] 2 2
[1] FALSE
D59V8, binary
                 cls
clus               0  1
  GPR98 MUTATED    6  1
  GPR98 WILD-TYPE 88 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED      6    1
  GPR98 WILD-TYPE   88   35
     clus
vv    GPR98 MUTATED GPR98 WILD-TYPE
  NO              6              88
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPR98 MUTATED                                     8
  GPR98 WILD-TYPE                                 122
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPR98 MUTATED                                       0
  GPR98 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPR98 MUTATED                                                  0
  GPR98 WILD-TYPE                                                2
D59V9, 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                          122
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D59V10, continuous
D59V11, continuous
                 vv
clus              R0 R1 R2 RX
  GPR98 MUTATED    6  1  0  1
  GPR98 WILD-TYPE 73 49  4  2
D59V12, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  R0             6              73
  R1             1              49
  R2             0               4
  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"
D59V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR98 MUTATED       0                         2     5
  GPR98 WILD-TYPE     9                         3   123
D59V14, multiclass
                           clus
vv                          GPR98 MUTATED GPR98 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                 5             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"
D59V15, binary
                 cls
clus               0  1
  GPR98 MUTATED    0  7
  GPR98 WILD-TYPE  5 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED      0    7
  GPR98 WILD-TYPE    5   98
                        clus
vv                       GPR98 MUTATED GPR98 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              98
[1] 2 2
[1] FALSE

Clustering(60) Variable = DAAM1 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2              0  1
  DAAM1 MUTATED    1  5
  DAAM1 WILD-TYPE 67 71
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              6             138 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              5              71 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
       20.19        23.21        12.03        19.59         9.83        12.43 
TCGA-HZ-8519 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK 
       14.93        21.70        16.14        10.13         6.38        21.60 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-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 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  DAAM1 MUTATED DAAM1 WILD-TYPE 
           3.62            0.03 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
          23.80           75.12 
  DAAM1 MUTATED DAAM1 WILD-TYPE 
         17.475          14.155 
[1] "3.6 - 23.8 (17.5)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.7"
D60V2, 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        3        8        23        98         4        3
D60V3, multiclass
           clus
vv          DAAM1 MUTATED DAAM1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              1               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
  DAAM1 MUTATED     0   0     6
  DAAM1 WILD-TYPE   4  16   119
D60V4, multiclass
       clus
vv      DAAM1 MUTATED DAAM1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D60V5, binary
                 cls
clus                0   1
  DAAM1 MUTATED     1   5
  DAAM1 WILD-TYPE  36 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      1    5
  DAAM1 WILD-TYPE   36  103
   clus
vv  DAAM1 MUTATED DAAM1 WILD-TYPE
  0             1              36
  1             5             103
[1] 2 2
[1] FALSE
D60V6, binary
                 cls
clus               0  1
  DAAM1 MUTATED    3  1
  DAAM1 WILD-TYPE 63  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      3    1
  DAAM1 WILD-TYPE   63    3
   clus
vv  DAAM1 MUTATED DAAM1 WILD-TYPE
  0             3              63
  1             1               3
[1] 2 2
[1] FALSE
D60V7, binary
                 cls
clus               0  1
  DAAM1 MUTATED    4  2
  DAAM1 WILD-TYPE 63 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      4    2
  DAAM1 WILD-TYPE   63   77
        clus
vv       DAAM1 MUTATED DAAM1 WILD-TYPE
  FEMALE             4              63
  MALE               2              77
[1] 2 2
[1] FALSE
D60V8, binary
                 cls
clus               0  1
  DAAM1 MUTATED    4  0
  DAAM1 WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      4    0
  DAAM1 WILD-TYPE   90   36
     clus
vv    DAAM1 MUTATED DAAM1 WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DAAM1 MUTATED                                     6
  DAAM1 WILD-TYPE                                 124
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DAAM1 MUTATED                                       0
  DAAM1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DAAM1 MUTATED                                                  0
  DAAM1 WILD-TYPE                                                2
D60V9, 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                          124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D60V10, continuous
[1] "Remove cluster labels:" "DAAM1 MUTATED"         
clus
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-IB-AAUU      TCGA-LB-A7SX 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
D60V11, continuous
[1] "Remove cluster labels:" "DAAM1 MUTATED"         
clus
  DAAM1 MUTATED DAAM1 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" "DAAM1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  DAAM1 MUTATED    1  4  0  1
  DAAM1 WILD-TYPE 78 46  4  2
D60V12, multiclass
    clus
vv   DAAM1 MUTATED DAAM1 WILD-TYPE
  R0             1              78
  R1             4              46
  R2             0               4
  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"
D60V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DAAM1 MUTATED       1                         1     4
  DAAM1 WILD-TYPE     8                         4   124
D60V14, multiclass
                           clus
vv                          DAAM1 MUTATED DAAM1 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                 cls
clus               0  1
  DAAM1 MUTATED    0  6
  DAAM1 WILD-TYPE  5 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAAM1 MUTATED      0    6
  DAAM1 WILD-TYPE    5   99
                        clus
vv                       DAAM1 MUTATED DAAM1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              99
[1] 2 2
[1] FALSE

Clustering(61) Variable = MTBP MUTATION ANALYSIS
D61V1, survival
                sevent
clus2             0  1
  MTBP MUTATED    1  2
  MTBP WILD-TYPE 67 74
  MTBP MUTATED MTBP WILD-TYPE 
             3            141 
  MTBP MUTATED MTBP WILD-TYPE 
             2             74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        12.95        49.38         4.77        21.90 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 
       19.82        23.80        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-AAUT TCGA-IB-AAUU TCGA-LB-A7SX 
       14.17         6.02        11.11         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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  MTBP MUTATED MTBP WILD-TYPE 
          3.62           0.03 
  MTBP MUTATED MTBP WILD-TYPE 
         15.35          75.12 
  MTBP MUTATED MTBP WILD-TYPE 
           7.4           14.4 
[1] "3.6 - 15.3 (7.4)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "3"  
D61V2, 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        3        8        23       100         4        4
D61V3, multiclass
           clus
vv          MTBP MUTATED MTBP WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   122
D61V4, multiclass
       clus
vv      MTBP MUTATED MTBP WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D61V5, binary
                cls
clus               0   1
  MTBP MUTATED     0   3
  MTBP WILD-TYPE  37 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTBP MUTATED      0    3
  MTBP WILD-TYPE   37  105
   clus
vv  MTBP MUTATED MTBP WILD-TYPE
  0            0             37
  1            3            105
[1] 2 2
[1] FALSE
D61V6, binary
                cls
clus              0  1
  MTBP MUTATED    3  0
  MTBP WILD-TYPE 63  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTBP MUTATED      3    0
  MTBP WILD-TYPE   63    4
   clus
vv  MTBP MUTATED MTBP WILD-TYPE
  0            3             63
  1            0              4
[1] 2 2
[1] FALSE
D61V7, binary
                cls
clus              0  1
  MTBP MUTATED    3  0
  MTBP WILD-TYPE 64 79
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTBP MUTATED      3    0
  MTBP WILD-TYPE   64   79
        clus
vv       MTBP MUTATED MTBP WILD-TYPE
  FEMALE            3             64
  MALE              0             79
[1] 2 2
[1] FALSE
D61V8, binary
                cls
clus              0  1
  MTBP MUTATED    3  0
  MTBP WILD-TYPE 91 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTBP MUTATED      3    0
  MTBP WILD-TYPE   91   36
     clus
vv    MTBP MUTATED MTBP WILD-TYPE
  NO             3             91
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MTBP MUTATED                                     3
  MTBP WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MTBP MUTATED                                       0
  MTBP WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MTBP MUTATED                                                  0
  MTBP WILD-TYPE                                                2
D61V9, multiclass
                                                  clus
vv                                                 MTBP MUTATED MTBP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D61V10, continuous
D61V11, continuous
[1] "Remove cluster labels:" "MTBP MUTATED"          
clus
  MTBP MUTATED MTBP WILD-TYPE 
             2             38 
    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-XN-A8T5     TCGA-YY-A8LH 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MTBP MUTATED    0  3  0  0
  MTBP WILD-TYPE 79 47  4  3
D61V12, multiclass
    clus
vv   MTBP MUTATED MTBP WILD-TYPE
  R0            0             79
  R1            3             47
  R2            0              4
  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"
D61V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTBP MUTATED       0                         0     2
  MTBP WILD-TYPE     9                         5   126
D61V14, multiclass
[1] "Remove cluster labels:" "MTBP MUTATED"          
clus
  MTBP MUTATED MTBP WILD-TYPE 
             2            140 
    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-HV-A5A3 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HV-A5A4     TCGA-HV-A5A5     TCGA-HV-A5A6     TCGA-HV-A7OL 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HV-AA8V     TCGA-HV-AA8X     TCGA-HZ-7919     TCGA-HZ-7922 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-7925     TCGA-HZ-7926     TCGA-HZ-8001     TCGA-HZ-8002 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-8003     TCGA-HZ-8005     TCGA-HZ-8315     TCGA-HZ-8317 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-8519     TCGA-HZ-8636     TCGA-HZ-8637     TCGA-HZ-A49G 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-A49H     TCGA-HZ-A49I     TCGA-HZ-A4BH     TCGA-HZ-A4BK 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-A77O     TCGA-HZ-A77P     TCGA-HZ-A77Q     TCGA-HZ-A8P0 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-HZ-A8P1     TCGA-HZ-A9TJ     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-XN-A8T3     TCGA-XN-A8T5 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
    TCGA-YB-A89D     TCGA-YH-A8SY     TCGA-YY-A8LH     TCGA-Z5-AAPL 
"MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" "MTBP WILD-TYPE" 
D61V15, binary
                cls
clus               0   1
  MTBP MUTATED     0   2
  MTBP WILD-TYPE   5 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTBP MUTATED      0    2
  MTBP WILD-TYPE    5  103
                        clus
vv                       MTBP MUTATED MTBP WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            2            103
[1] 2 2
[1] FALSE

Clustering(62) Variable = RREB1 MUTATION ANALYSIS
D62V1, survival
                 sevent
clus2              0  1
  RREB1 MUTATED    3  6
  RREB1 WILD-TYPE 65 70
  RREB1 MUTATED RREB1 WILD-TYPE 
              9             135 
  RREB1 MUTATED RREB1 WILD-TYPE 
              6              70 
$`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        42.31        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 
       58.98        43.50         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 
       17.49        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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
        2.47        17.16        12.00         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-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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  RREB1 MUTATED RREB1 WILD-TYPE 
           7.50            0.03 
  RREB1 MUTATED RREB1 WILD-TYPE 
          43.79           75.12 
  RREB1 MUTATED RREB1 WILD-TYPE 
          17.03           14.14 
[1] "7.5 - 43.8 (17.0)" "0.0 - 75.1 (14.1)"
[1] "hr=" "1.1"
D62V2, 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        3        8        19        98         4        4
D62V3, multiclass
           clus
vv          RREB1 MUTATED RREB1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             4              19
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              0               4
[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   4  15   117
D62V4, multiclass
       clus
vv      RREB1 MUTATED RREB1 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D62V5, binary
                 cls
clus                0   1
  RREB1 MUTATED     4   5
  RREB1 WILD-TYPE  33 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      4    5
  RREB1 WILD-TYPE   33  103
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0             4              33
  1             5             103
[1] 2 2
[1] FALSE
D62V6, binary
                 cls
clus               0  1
  RREB1 MUTATED    5  0
  RREB1 WILD-TYPE 61  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      5    0
  RREB1 WILD-TYPE   61    4
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0             5              61
  1             0               4
[1] 2 2
[1] FALSE
D62V7, binary
                 cls
clus               0  1
  RREB1 MUTATED    3  6
  RREB1 WILD-TYPE 64 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      3    6
  RREB1 WILD-TYPE   64   73
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  FEMALE             3              64
  MALE               6              73
[1] 2 2
[1] FALSE
D62V8, binary
                 cls
clus               0  1
  RREB1 MUTATED    4  4
  RREB1 WILD-TYPE 90 32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      4    4
  RREB1 WILD-TYPE   90   32
     clus
vv    RREB1 MUTATED RREB1 WILD-TYPE
  NO              4              90
  YES             4              32
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RREB1 MUTATED                                     9
  RREB1 WILD-TYPE                                 121
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RREB1 MUTATED                                       0
  RREB1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RREB1 MUTATED                                                  0
  RREB1 WILD-TYPE                                                2
D62V9, 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                          121
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D62V10, continuous
D62V11, continuous
                 vv
clus              R0 R1 R2 RX
  RREB1 MUTATED    6  2  0  1
  RREB1 WILD-TYPE 73 48  4  2
D62V12, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  R0             6              73
  R1             2              48
  R2             0               4
  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"
D62V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RREB1 MUTATED       0                         2     7
  RREB1 WILD-TYPE     9                         3   121
D62V14, multiclass
                           clus
vv                          RREB1 MUTATED RREB1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             2               3
  WHITE                                 7             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"
D62V15, binary
                 cls
clus               0  1
  RREB1 MUTATED    0  7
  RREB1 WILD-TYPE  5 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      0    7
  RREB1 WILD-TYPE    5   98
                        clus
vv                       RREB1 MUTATED RREB1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              98
[1] 2 2
[1] FALSE

Clustering(63) Variable = TRPC4 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2              0  1
  TRPC4 MUTATED    3  3
  TRPC4 WILD-TYPE 65 73
  TRPC4 MUTATED TRPC4 WILD-TYPE 
              6             138 
  TRPC4 MUTATED TRPC4 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-A9TJ TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08        19.82        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-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 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  TRPC4 MUTATED TRPC4 WILD-TYPE 
           0.23            0.03 
  TRPC4 MUTATED TRPC4 WILD-TYPE 
          19.82           75.12 
  TRPC4 MUTATED TRPC4 WILD-TYPE 
          9.860          14.435 
[1] "0.2 - 19.8 (9.9)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "1.7"
D63V2, 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        3        7        22       100         3        4
D63V3, multiclass
           clus
vv          TRPC4 MUTATED TRPC4 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             1              22
  STAGE IIB             3             100
  STAGE III             1               3
  STAGE IV              0               4
[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   4  15   120
D63V4, multiclass
       clus
vv      TRPC4 MUTATED TRPC4 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D63V5, binary
                 cls
clus                0   1
  TRPC4 MUTATED     2   4
  TRPC4 WILD-TYPE  35 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC4 MUTATED      2    4
  TRPC4 WILD-TYPE   35  104
   clus
vv  TRPC4 MUTATED TRPC4 WILD-TYPE
  0             2              35
  1             4             104
[1] 2 2
[1] FALSE
D63V6, binary
                 cls
clus               0  1
  TRPC4 MUTATED    3  0
  TRPC4 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC4 MUTATED      3    0
  TRPC4 WILD-TYPE   63    4
   clus
vv  TRPC4 MUTATED TRPC4 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D63V7, binary
                 cls
clus               0  1
  TRPC4 MUTATED    4  2
  TRPC4 WILD-TYPE 63 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC4 MUTATED      4    2
  TRPC4 WILD-TYPE   63   77
        clus
vv       TRPC4 MUTATED TRPC4 WILD-TYPE
  FEMALE             4              63
  MALE               2              77
[1] 2 2
[1] FALSE
D63V8, binary
                 cls
clus               0  1
  TRPC4 MUTATED    3  0
  TRPC4 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC4 MUTATED      3    0
  TRPC4 WILD-TYPE   91   36
     clus
vv    TRPC4 MUTATED TRPC4 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TRPC4 MUTATED                                     5
  TRPC4 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TRPC4 MUTATED                                       1
  TRPC4 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TRPC4 MUTATED                                                  0
  TRPC4 WILD-TYPE                                                2
D63V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D63V10, continuous
D63V11, continuous
                 vv
clus              R0 R1 R2 RX
  TRPC4 MUTATED    3  2  0  0
  TRPC4 WILD-TYPE 76 48  4  3
D63V12, multiclass
    clus
vv   TRPC4 MUTATED TRPC4 WILD-TYPE
  R0             3              76
  R1             2              48
  R2             0               4
  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"
D63V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRPC4 MUTATED       0                         0     6
  TRPC4 WILD-TYPE     9                         5   122
D63V14, multiclass
                           clus
vv                          TRPC4 MUTATED TRPC4 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             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"
D63V15, binary
                 cls
clus               0  1
  TRPC4 MUTATED    0  6
  TRPC4 WILD-TYPE  5 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPC4 MUTATED      0    6
  TRPC4 WILD-TYPE    5   99
                        clus
vv                       TRPC4 MUTATED TRPC4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              99
[1] 2 2
[1] FALSE

Clustering(64) Variable = CD2AP MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2              0  1
  CD2AP MUTATED    0  3
  CD2AP WILD-TYPE 68 73
  CD2AP MUTATED CD2AP WILD-TYPE 
              3             141 
  CD2AP MUTATED CD2AP WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
       20.19        17.03        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        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-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-AAUP 
        1.35         8.22        15.88         0.26         4.73        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  CD2AP MUTATED CD2AP WILD-TYPE 
           3.95            0.03 
  CD2AP MUTATED CD2AP WILD-TYPE 
          19.82           75.12 
  CD2AP MUTATED CD2AP WILD-TYPE 
           7.86           14.40 
[1] "4.0 - 19.8 (7.9)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "3.2"
D64V2, 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        3        8        23       100         4        4
D64V3, multiclass
           clus
vv          CD2AP MUTATED CD2AP WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D64V4, multiclass
       clus
vv      CD2AP MUTATED CD2AP WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D64V5, binary
                 cls
clus                0   1
  CD2AP MUTATED     0   3
  CD2AP WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD2AP MUTATED      0    3
  CD2AP WILD-TYPE   37  105
   clus
vv  CD2AP MUTATED CD2AP WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D64V6, binary
                 cls
clus               0  1
  CD2AP MUTATED    2  0
  CD2AP WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD2AP MUTATED      2    0
  CD2AP WILD-TYPE   64    4
   clus
vv  CD2AP MUTATED CD2AP WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D64V7, binary
                 cls
clus               0  1
  CD2AP MUTATED    2  1
  CD2AP WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD2AP MUTATED      2    1
  CD2AP WILD-TYPE   65   78
        clus
vv       CD2AP MUTATED CD2AP WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D64V8, binary
                 cls
clus               0  1
  CD2AP MUTATED    3  0
  CD2AP WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD2AP MUTATED      3    0
  CD2AP WILD-TYPE   91   36
     clus
vv    CD2AP MUTATED CD2AP WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD2AP MUTATED                                     3
  CD2AP WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD2AP MUTATED                                       0
  CD2AP WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD2AP MUTATED                                                  0
  CD2AP WILD-TYPE                                                2
D64V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D64V10, continuous
[1] "Remove cluster labels:" "CD2AP MUTATED"         
clus
  CD2AP MUTATED CD2AP WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
     TCGA-YY-A8LH 
"CD2AP WILD-TYPE" 
D64V11, continuous
[1] "Remove cluster labels:" "CD2AP MUTATED"         
clus
  CD2AP MUTATED CD2AP WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"CD2AP WILD-TYPE" "CD2AP WILD-TYPE" "CD2AP WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CD2AP MUTATED    1  2  0  0
  CD2AP WILD-TYPE 78 48  4  3
D64V12, multiclass
    clus
vv   CD2AP MUTATED CD2AP WILD-TYPE
  R0             1              78
  R1             2              48
  R2             0               4
  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"
D64V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD2AP MUTATED       0                         0     3
  CD2AP WILD-TYPE     9                         5   125
D64V14, multiclass
                           clus
vv                          CD2AP MUTATED CD2AP WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, binary
                 cls
clus                0   1
  CD2AP MUTATED     0   3
  CD2AP WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD2AP MUTATED      0    3
  CD2AP WILD-TYPE    5  102
                        clus
vv                       CD2AP MUTATED CD2AP WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(65) Variable = GNAS MUTATION ANALYSIS
D65V1, survival
                sevent
clus2             0  1
  GNAS MUTATED    3  6
  GNAS WILD-TYPE 65 70
  GNAS MUTATED GNAS WILD-TYPE 
             9            135 
  GNAS MUTATED GNAS WILD-TYPE 
             6             70 
$`GNAS MUTATED`
TCGA-2J-AAB1 TCGA-F2-A44G TCGA-HV-AA8V TCGA-HZ-8317 TCGA-IB-7651 TCGA-IB-A5SO 
        2.17         7.66        30.25        12.43        19.82        12.00 
TCGA-IB-AAUT TCGA-US-A776 TCGA-US-A77E 
        9.44        39.98        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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
       15.98         2.47        17.16        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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG 
       17.26        23.08        22.85        16.80         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  GNAS MUTATED GNAS WILD-TYPE 
          2.17           0.03 
  GNAS MUTATED GNAS WILD-TYPE 
         39.98          75.12 
  GNAS MUTATED GNAS WILD-TYPE 
         12.43          14.47 
[1] "2.2 - 40.0 (12.4)" "0.0 - 75.1 (14.5)"
[1] "hr=" "1.4"
D65V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GNAS MUTATED          0        0         1         8         0        0
  GNAS WILD-TYPE        3        8        22        95         4        4
D65V3, multiclass
           clus
vv          GNAS MUTATED GNAS WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            1             22
  STAGE IIB            8             95
  STAGE III            0              4
  STAGE IV             0              4
[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     8
  GNAS WILD-TYPE   4  15   117
D65V4, multiclass
       clus
vv      GNAS MUTATED GNAS WILD-TYPE
  T1               0              4
  T2               1             15
  T3+T4            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"
D65V5, binary
                cls
clus               0   1
  GNAS MUTATED     1   8
  GNAS WILD-TYPE  36 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      1    8
  GNAS WILD-TYPE   36  100
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            1             36
  1            8            100
[1] 2 2
[1] FALSE
D65V6, binary
                cls
clus              0  1
  GNAS MUTATED    5  0
  GNAS WILD-TYPE 61  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      5    0
  GNAS WILD-TYPE   61    4
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            5             61
  1            0              4
[1] 2 2
[1] FALSE
D65V7, binary
                cls
clus              0  1
  GNAS MUTATED    3  6
  GNAS WILD-TYPE 64 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      3    6
  GNAS WILD-TYPE   64   73
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE            3             64
  MALE              6             73
[1] 2 2
[1] FALSE
D65V8, binary
                cls
clus              0  1
  GNAS MUTATED    7  2
  GNAS WILD-TYPE 87 34
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      7    2
  GNAS WILD-TYPE   87   34
     clus
vv    GNAS MUTATED GNAS WILD-TYPE
  NO             7             87
  YES            2             34
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GNAS MUTATED                                     5
  GNAS WILD-TYPE                                 125
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GNAS MUTATED                                       2
  GNAS WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GNAS MUTATED                                                  2
  GNAS WILD-TYPE                                                0
D65V9, multiclass
                                                  clus
vv                                                 GNAS MUTATED GNAS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             11
  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"
D65V10, continuous
D65V11, continuous
                vv
clus             R0 R1 R2 RX
  GNAS MUTATED    4  4  1  0
  GNAS WILD-TYPE 75 46  3  3
D65V12, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0            4             75
  R1            4             46
  R2            1              3
  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"
D65V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNAS MUTATED       1                         0     8
  GNAS WILD-TYPE     8                         5   120
D65V14, multiclass
                           clus
vv                          GNAS MUTATED GNAS WILD-TYPE
  ASIAN                                1              8
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                8            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"
D65V15, binary
                cls
clus              0  1
  GNAS MUTATED    0  6
  GNAS WILD-TYPE  5 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      0    6
  GNAS WILD-TYPE    5   99
                        clus
vv                       GNAS MUTATED GNAS WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             99
[1] 2 2
[1] FALSE

Clustering(66) Variable = FAR1 MUTATION ANALYSIS
D66V1, survival
                sevent
clus2             0  1
  FAR1 MUTATED    2  2
  FAR1 WILD-TYPE 66 74
  FAR1 MUTATED FAR1 WILD-TYPE 
             4            140 
  FAR1 MUTATED FAR1 WILD-TYPE 
             2             74 
$`FAR1 MUTATED`
TCGA-3A-A9J0 TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7885 
       24.43        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3E-AAAY TCGA-3E-AAAZ 
       33.57        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  FAR1 MUTATED FAR1 WILD-TYPE 
         19.82           0.03 
  FAR1 MUTATED FAR1 WILD-TYPE 
         41.33          75.12 
  FAR1 MUTATED FAR1 WILD-TYPE 
         22.31          13.99 
[1] "19.8 - 41.3 (22.3)" "0.0 - 75.1 (14.0)" 
[1] "hr=" "1.9"
D66V2, 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        3        8        23        99         4        4
D66V3, multiclass
           clus
vv          FAR1 MUTATED FAR1 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            4             99
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   121
D66V4, multiclass
       clus
vv      FAR1 MUTATED FAR1 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D66V5, binary
                cls
clus               0   1
  FAR1 MUTATED     0   4
  FAR1 WILD-TYPE  37 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAR1 MUTATED      0    4
  FAR1 WILD-TYPE   37  104
   clus
vv  FAR1 MUTATED FAR1 WILD-TYPE
  0            0             37
  1            4            104
[1] 2 2
[1] FALSE
D66V6, binary
                cls
clus              0  1
  FAR1 MUTATED    2  0
  FAR1 WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAR1 MUTATED      2    0
  FAR1 WILD-TYPE   64    4
   clus
vv  FAR1 MUTATED FAR1 WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D66V7, binary
                cls
clus              0  1
  FAR1 MUTATED    2  2
  FAR1 WILD-TYPE 65 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAR1 MUTATED      2    2
  FAR1 WILD-TYPE   65   77
        clus
vv       FAR1 MUTATED FAR1 WILD-TYPE
  FEMALE            2             65
  MALE              2             77
[1] 2 2
[1] FALSE
D66V8, binary
                cls
clus              0  1
  FAR1 MUTATED    4  0
  FAR1 WILD-TYPE 90 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAR1 MUTATED      4    0
  FAR1 WILD-TYPE   90   36
     clus
vv    FAR1 MUTATED FAR1 WILD-TYPE
  NO             4             90
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAR1 MUTATED                                     4
  FAR1 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAR1 MUTATED                                       0
  FAR1 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAR1 MUTATED                                                  0
  FAR1 WILD-TYPE                                                2
D66V9, multiclass
                                                  clus
vv                                                 FAR1 MUTATED FAR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D66V10, continuous
[1] "Remove cluster labels:" "FAR1 MUTATED"          
clus
  FAR1 MUTATED FAR1 WILD-TYPE 
             2             48 
    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-HV-AA8V     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-7887 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
D66V11, continuous
[1] "Remove cluster labels:" "FAR1 MUTATED"          
clus
  FAR1 MUTATED FAR1 WILD-TYPE 
             2             38 
    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-XN-A8T5     TCGA-YY-A8LH 
"FAR1 WILD-TYPE" "FAR1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  FAR1 MUTATED    4  0  0  0
  FAR1 WILD-TYPE 75 50  4  3
D66V12, multiclass
    clus
vv   FAR1 MUTATED FAR1 WILD-TYPE
  R0            4             75
  R1            0             50
  R2            0              4
  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"
D66V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAR1 MUTATED       0                         0     4
  FAR1 WILD-TYPE     9                         5   124
D66V14, multiclass
                           clus
vv                          FAR1 MUTATED FAR1 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, binary
                cls
clus               0   1
  FAR1 MUTATED     0   4
  FAR1 WILD-TYPE   5 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAR1 MUTATED      0    4
  FAR1 WILD-TYPE    5  101
                        clus
vv                       FAR1 MUTATED FAR1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(67) Variable = COL28A1 MUTATION ANALYSIS
D67V1, survival
                   sevent
clus2                0  1
  COL28A1 MUTATED    2  3
  COL28A1 WILD-TYPE 66 73
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                5               139 
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                3                73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH 
       12.03        16.37        31.27        23.67        11.51        66.28 
TCGA-Z5-AAPL 
       15.35 

  COL28A1 MUTATED COL28A1 WILD-TYPE 
            12.76              0.03 
  COL28A1 MUTATED COL28A1 WILD-TYPE 
            41.33             75.12 
  COL28A1 MUTATED COL28A1 WILD-TYPE 
            19.82             14.14 
[1] "12.8 - 41.3 (19.8)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "1.2"
D67V2, 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        3        8        23        99         3        4
D67V3, multiclass
           clus
vv          COL28A1 MUTATED COL28A1 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               0                23
  STAGE IIB               4                99
  STAGE III               1                 3
  STAGE IV                0                 4
[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   4  16   120
D67V4, multiclass
       clus
vv      COL28A1 MUTATED COL28A1 WILD-TYPE
  T1                  0                 4
  T2                  0                16
  T3+T4               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"
D67V5, binary
                   cls
clus                  0   1
  COL28A1 MUTATED     0   5
  COL28A1 WILD-TYPE  37 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL28A1 MUTATED      0    5
  COL28A1 WILD-TYPE   37  103
   clus
vv  COL28A1 MUTATED COL28A1 WILD-TYPE
  0               0                37
  1               5               103
[1] 2 2
[1] FALSE
D67V6, binary
                   cls
clus                 0  1
  COL28A1 MUTATED    2  0
  COL28A1 WILD-TYPE 64  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL28A1 MUTATED      2    0
  COL28A1 WILD-TYPE   64    4
   clus
vv  COL28A1 MUTATED COL28A1 WILD-TYPE
  0               2                64
  1               0                 4
[1] 2 2
[1] FALSE
D67V7, binary
                   cls
clus                 0  1
  COL28A1 MUTATED    3  2
  COL28A1 WILD-TYPE 64 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL28A1 MUTATED      3    2
  COL28A1 WILD-TYPE   64   77
        clus
vv       COL28A1 MUTATED COL28A1 WILD-TYPE
  FEMALE               3                64
  MALE                 2                77
[1] 2 2
[1] FALSE
D67V8, binary
                   cls
clus                 0  1
  COL28A1 MUTATED    3  1
  COL28A1 WILD-TYPE 91 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL28A1 MUTATED      3    1
  COL28A1 WILD-TYPE   91   35
     clus
vv    COL28A1 MUTATED COL28A1 WILD-TYPE
  NO                3                91
  YES               1                35
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  COL28A1 MUTATED                                     4
  COL28A1 WILD-TYPE                                 126
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  COL28A1 MUTATED                                       0
  COL28A1 WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  COL28A1 MUTATED                                                  0
  COL28A1 WILD-TYPE                                                2
D67V9, 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                            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D67V10, continuous
[1] "Remove cluster labels:" "COL28A1 MUTATED"       
clus
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                2                48 
       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-HV-AA8V        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-7887 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
D67V11, continuous
[1] "Remove cluster labels:" "COL28A1 MUTATED"       
clus
  COL28A1 MUTATED COL28A1 WILD-TYPE 
                2                38 
       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-XN-A8T5        TCGA-YY-A8LH 
"COL28A1 WILD-TYPE" "COL28A1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  COL28A1 MUTATED    3  0  0  1
  COL28A1 WILD-TYPE 76 50  4  2
D67V12, multiclass
    clus
vv   COL28A1 MUTATED COL28A1 WILD-TYPE
  R0               3                76
  R1               0                50
  R2               0                 4
  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"
D67V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COL28A1 MUTATED       0                         1     4
  COL28A1 WILD-TYPE     9                         4   124
D67V14, multiclass
                           clus
vv                          COL28A1 MUTATED COL28A1 WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   4               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V15, binary
                   cls
clus                  0   1
  COL28A1 MUTATED     0   5
  COL28A1 WILD-TYPE   5 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL28A1 MUTATED      0    5
  COL28A1 WILD-TYPE    5  100
                        clus
vv                       COL28A1 MUTATED COL28A1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5               100
[1] 2 2
[1] FALSE

Clustering(68) Variable = SKA3 MUTATION ANALYSIS
D68V1, survival
                sevent
clus2             0  1
  SKA3 MUTATED    4  2
  SKA3 WILD-TYPE 64 74
  SKA3 MUTATED SKA3 WILD-TYPE 
             6            138 
  SKA3 MUTATED SKA3 WILD-TYPE 
             2             74 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
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-A6UG TCGA-IB-A7LX 
       15.85         7.20        15.12        20.88         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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YY-A8LH TCGA-Z5-AAPL 
       16.37        31.27        23.67        11.51        66.28        15.35 

  SKA3 MUTATED SKA3 WILD-TYPE 
          3.12           0.03 
  SKA3 MUTATED SKA3 WILD-TYPE 
         23.80          75.12 
  SKA3 MUTATED SKA3 WILD-TYPE 
        20.860         14.155 
[1] "3.1 - 23.8 (20.9)" "0.0 - 75.1 (14.2)"
[1] "hr=" "2.1"
D68V2, 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        3        7        23        99         3        4
D68V3, multiclass
           clus
vv          SKA3 MUTATED SKA3 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             1              7
  STAGE IIA            0             23
  STAGE IIB            4             99
  STAGE III            1              3
  STAGE IV             0              4
[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   4  16   119
D68V4, multiclass
       clus
vv      SKA3 MUTATED SKA3 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D68V5, binary
                cls
clus               0   1
  SKA3 MUTATED     0   6
  SKA3 WILD-TYPE  37 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      0    6
  SKA3 WILD-TYPE   37  102
   clus
vv  SKA3 MUTATED SKA3 WILD-TYPE
  0            0             37
  1            6            102
[1] 2 2
[1] FALSE
D68V6, binary
                cls
clus              0  1
  SKA3 MUTATED    4  0
  SKA3 WILD-TYPE 62  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      4    0
  SKA3 WILD-TYPE   62    4
   clus
vv  SKA3 MUTATED SKA3 WILD-TYPE
  0            4             62
  1            0              4
[1] 2 2
[1] FALSE
D68V7, binary
                cls
clus              0  1
  SKA3 MUTATED    4  2
  SKA3 WILD-TYPE 63 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      4    2
  SKA3 WILD-TYPE   63   77
        clus
vv       SKA3 MUTATED SKA3 WILD-TYPE
  FEMALE            4             63
  MALE              2             77
[1] 2 2
[1] FALSE
D68V8, binary
                cls
clus              0  1
  SKA3 MUTATED    4  2
  SKA3 WILD-TYPE 90 34
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      4    2
  SKA3 WILD-TYPE   90   34
     clus
vv    SKA3 MUTATED SKA3 WILD-TYPE
  NO             4             90
  YES            2             34
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SKA3 MUTATED                                     5
  SKA3 WILD-TYPE                                 125
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SKA3 MUTATED                                       0
  SKA3 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SKA3 MUTATED                                                  0
  SKA3 WILD-TYPE                                                2
D68V9, multiclass
                                                  clus
vv                                                 SKA3 MUTATED SKA3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D68V10, continuous
D68V11, continuous
                vv
clus             R0 R1 R2 RX
  SKA3 MUTATED    1  3  0  1
  SKA3 WILD-TYPE 78 47  4  2
D68V12, multiclass
    clus
vv   SKA3 MUTATED SKA3 WILD-TYPE
  R0            1             78
  R1            3             47
  R2            0              4
  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"
D68V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SKA3 MUTATED       1                         0     5
  SKA3 WILD-TYPE     8                         5   123
D68V14, multiclass
                           clus
vv                          SKA3 MUTATED SKA3 WILD-TYPE
  ASIAN                                1              8
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            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"
D68V15, binary
                cls
clus               0   1
  SKA3 MUTATED     0   5
  SKA3 WILD-TYPE   5 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      0    5
  SKA3 WILD-TYPE    5  100
                        clus
vv                       SKA3 MUTATED SKA3 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5            100
[1] 2 2
[1] FALSE

Clustering(69) Variable = JAK2 MUTATION ANALYSIS
D69V1, survival
                sevent
clus2             0  1
  JAK2 MUTATED    1  3
  JAK2 WILD-TYPE 67 73
  JAK2 MUTATED JAK2 WILD-TYPE 
             4            140 
  JAK2 MUTATED JAK2 WILD-TYPE 
             3             73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       17.03        23.21        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  JAK2 MUTATED JAK2 WILD-TYPE 
         12.03           0.03 
  JAK2 MUTATED JAK2 WILD-TYPE 
         41.33          75.12 
  JAK2 MUTATED JAK2 WILD-TYPE 
        20.005         14.155 
[1] "12.0 - 41.3 (20.0)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "1"  
D69V2, 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        3        8        23        99         4        4
D69V3, multiclass
           clus
vv          JAK2 MUTATED JAK2 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            4             99
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   121
D69V4, multiclass
       clus
vv      JAK2 MUTATED JAK2 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D69V5, binary
                cls
clus               0   1
  JAK2 MUTATED     0   4
  JAK2 WILD-TYPE  37 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED      0    4
  JAK2 WILD-TYPE   37  104
   clus
vv  JAK2 MUTATED JAK2 WILD-TYPE
  0            0             37
  1            4            104
[1] 2 2
[1] FALSE
D69V6, binary
                cls
clus              0  1
  JAK2 MUTATED    2  0
  JAK2 WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED      2    0
  JAK2 WILD-TYPE   64    4
   clus
vv  JAK2 MUTATED JAK2 WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D69V7, binary
                cls
clus              0  1
  JAK2 MUTATED    2  2
  JAK2 WILD-TYPE 65 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED      2    2
  JAK2 WILD-TYPE   65   77
        clus
vv       JAK2 MUTATED JAK2 WILD-TYPE
  FEMALE            2             65
  MALE              2             77
[1] 2 2
[1] FALSE
D69V8, binary
                cls
clus              0  1
  JAK2 MUTATED    4  0
  JAK2 WILD-TYPE 90 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED      4    0
  JAK2 WILD-TYPE   90   36
     clus
vv    JAK2 MUTATED JAK2 WILD-TYPE
  NO             4             90
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  JAK2 MUTATED                                     4
  JAK2 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  JAK2 MUTATED                                       0
  JAK2 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  JAK2 MUTATED                                                  0
  JAK2 WILD-TYPE                                                2
D69V9, multiclass
                                                  clus
vv                                                 JAK2 MUTATED JAK2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D69V10, continuous
[1] "Remove cluster labels:" "JAK2 MUTATED"          
clus
  JAK2 MUTATED JAK2 WILD-TYPE 
             2             48 
    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-HV-AA8V     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-7887 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
D69V11, continuous
[1] "Remove cluster labels:" "JAK2 MUTATED"          
clus
  JAK2 MUTATED JAK2 WILD-TYPE 
             2             38 
    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-XN-A8T5     TCGA-YY-A8LH 
"JAK2 WILD-TYPE" "JAK2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  JAK2 MUTATED    4  0  0  0
  JAK2 WILD-TYPE 75 50  4  3
D69V12, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  R0            4             75
  R1            0             50
  R2            0              4
  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"
D69V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  JAK2 MUTATED       0                         0     4
  JAK2 WILD-TYPE     9                         5   124
D69V14, multiclass
                           clus
vv                          JAK2 MUTATED JAK2 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, binary
                cls
clus               0   1
  JAK2 MUTATED     0   4
  JAK2 WILD-TYPE   5 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED      0    4
  JAK2 WILD-TYPE    5  101
                        clus
vv                       JAK2 MUTATED JAK2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(70) Variable = ARID1A MUTATION ANALYSIS
D70V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    4  3
  ARID1A WILD-TYPE 64 73
  ARID1A MUTATED ARID1A WILD-TYPE 
               7              137 
  ARID1A MUTATED ARID1A WILD-TYPE 
               3               73 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-A9TJ TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         1.08        19.82        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-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 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        15.35 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.23             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
           66.28            75.12 
  ARID1A MUTATED ARID1A WILD-TYPE 
           19.82            14.17 
[1] "0.2 - 66.3 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.5"
D70V2, 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        3        7        23        98         3        4
D70V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE IA               0                3
  STAGE IB               1                7
  STAGE IIA              0               23
  STAGE IIB              5               98
  STAGE III              1                3
  STAGE IV               0                4
[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   4  15   119
D70V4, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  T1                 0                4
  T2                 1               15
  T3+T4              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"
D70V5, binary
                  cls
clus                 0   1
  ARID1A MUTATED     2   5
  ARID1A WILD-TYPE  35 103
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    5
  ARID1A WILD-TYPE   35  103
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              2               35
  1              5              103
[1] 2 2
[1] FALSE
D70V6, binary
                  cls
clus                0  1
  ARID1A MUTATED    4  0
  ARID1A WILD-TYPE 62  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      4    0
  ARID1A WILD-TYPE   62    4
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              4               62
  1              0                4
[1] 2 2
[1] FALSE
D70V7, binary
                  cls
clus                0  1
  ARID1A MUTATED    2  5
  ARID1A WILD-TYPE 65 74
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    5
  ARID1A WILD-TYPE   65   74
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              2               65
  MALE                5               74
[1] 2 2
[1] FALSE
D70V8, binary
                  cls
clus                0  1
  ARID1A MUTATED    5  1
  ARID1A WILD-TYPE 89 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    1
  ARID1A WILD-TYPE   89   35
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               5               89
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARID1A MUTATED                                     7
  ARID1A WILD-TYPE                                 123
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARID1A MUTATED                                       0
  ARID1A WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARID1A MUTATED                                                  0
  ARID1A WILD-TYPE                                                2
D70V9, 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                           123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D70V10, continuous
D70V11, continuous
                  vv
clus               R0 R1 R2 RX
  ARID1A MUTATED    4  3  0  0
  ARID1A WILD-TYPE 75 47  4  3
D70V12, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0              4               75
  R1              3               47
  R2              0                4
  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"
D70V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         0     7
  ARID1A WILD-TYPE     9                         5   121
D70V14, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  7              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"
D70V15, binary
                  cls
clus                 0   1
  ARID1A MUTATED     0   5
  ARID1A WILD-TYPE   5 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0    5
  ARID1A WILD-TYPE    5  100
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5              100
[1] 2 2
[1] FALSE

Clustering(71) Variable = KCNA7 MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2              0  1
  KCNA7 MUTATED    2  3
  KCNA7 WILD-TYPE 66 73
  KCNA7 MUTATED KCNA7 WILD-TYPE 
              5             139 
  KCNA7 MUTATED KCNA7 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7885 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       41.33         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80        14.14        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  KCNA7 MUTATED KCNA7 WILD-TYPE 
           0.39            0.03 
  KCNA7 MUTATED KCNA7 WILD-TYPE 
          23.80           75.12 
  KCNA7 MUTATED KCNA7 WILD-TYPE 
          11.93           14.40 
[1] "0.4 - 23.8 (11.9)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.4"
D71V2, 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        3        8        23        98         4        4
D71V3, multiclass
           clus
vv          KCNA7 MUTATED KCNA7 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   120
D71V4, multiclass
       clus
vv      KCNA7 MUTATED KCNA7 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D71V5, binary
                 cls
clus                0   1
  KCNA7 MUTATED     0   5
  KCNA7 WILD-TYPE  37 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA7 MUTATED      0    5
  KCNA7 WILD-TYPE   37  103
   clus
vv  KCNA7 MUTATED KCNA7 WILD-TYPE
  0             0              37
  1             5             103
[1] 2 2
[1] FALSE
D71V6, binary
                 cls
clus               0  1
  KCNA7 MUTATED    3  0
  KCNA7 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA7 MUTATED      3    0
  KCNA7 WILD-TYPE   63    4
   clus
vv  KCNA7 MUTATED KCNA7 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D71V7, binary
                 cls
clus               0  1
  KCNA7 MUTATED    2  3
  KCNA7 WILD-TYPE 65 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA7 MUTATED      2    3
  KCNA7 WILD-TYPE   65   76
        clus
vv       KCNA7 MUTATED KCNA7 WILD-TYPE
  FEMALE             2              65
  MALE               3              76
[1] 2 2
[1] FALSE
D71V8, binary
                 cls
clus               0  1
  KCNA7 MUTATED    4  1
  KCNA7 WILD-TYPE 90 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA7 MUTATED      4    1
  KCNA7 WILD-TYPE   90   35
     clus
vv    KCNA7 MUTATED KCNA7 WILD-TYPE
  NO              4              90
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KCNA7 MUTATED                                     5
  KCNA7 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KCNA7 MUTATED                                       0
  KCNA7 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KCNA7 MUTATED                                                  0
  KCNA7 WILD-TYPE                                                2
D71V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D71V10, continuous
D71V11, continuous
                 vv
clus              R0 R1 R2 RX
  KCNA7 MUTATED    2  2  0  0
  KCNA7 WILD-TYPE 77 48  4  3
D71V12, multiclass
    clus
vv   KCNA7 MUTATED KCNA7 WILD-TYPE
  R0             2              77
  R1             2              48
  R2             0               4
  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"
D71V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNA7 MUTATED       1                         0     4
  KCNA7 WILD-TYPE     8                         5   124
D71V14, multiclass
                           clus
vv                          KCNA7 MUTATED KCNA7 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, binary
                 cls
clus                0   1
  KCNA7 MUTATED     0   5
  KCNA7 WILD-TYPE   5 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA7 MUTATED      0    5
  KCNA7 WILD-TYPE    5  100
                        clus
vv                       KCNA7 MUTATED KCNA7 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             100
[1] 2 2
[1] FALSE

Clustering(72) Variable = CHRNA9 MUTATION ANALYSIS
D72V1, survival
                  sevent
clus2               0  1
  CHRNA9 MUTATED    1  3
  CHRNA9 WILD-TYPE 67 73
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               4              140 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               3               73 
$`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        42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX 
       43.50        20.84        24.26        33.57        15.06        34.09 
TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G 
       10.13        24.43        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-A6UG TCGA-IB-A7LX 
       15.85         7.20        15.12        20.88         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
            4.70             0.03 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
           21.90            75.12 
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
           8.480           14.435 
[1] "4.7 - 21.9 (8.5)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "2.2"
D72V2, 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        3        8        23        99         4        4
D72V3, multiclass
           clus
vv          CHRNA9 MUTATED CHRNA9 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              4               99
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   121
D72V4, multiclass
       clus
vv      CHRNA9 MUTATED CHRNA9 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D72V5, binary
                  cls
clus                 0   1
  CHRNA9 MUTATED     0   4
  CHRNA9 WILD-TYPE  37 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      0    4
  CHRNA9 WILD-TYPE   37  104
   clus
vv  CHRNA9 MUTATED CHRNA9 WILD-TYPE
  0              0               37
  1              4              104
[1] 2 2
[1] FALSE
D72V6, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    1  0
  CHRNA9 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      1    0
  CHRNA9 WILD-TYPE   65    4
   clus
vv  CHRNA9 MUTATED CHRNA9 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D72V7, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    1  3
  CHRNA9 WILD-TYPE 66 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      1    3
  CHRNA9 WILD-TYPE   66   76
        clus
vv       CHRNA9 MUTATED CHRNA9 WILD-TYPE
  FEMALE              1               66
  MALE                3               76
[1] 2 2
[1] FALSE
D72V8, binary
                  cls
clus                0  1
  CHRNA9 MUTATED    4  0
  CHRNA9 WILD-TYPE 90 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      4    0
  CHRNA9 WILD-TYPE   90   36
     clus
vv    CHRNA9 MUTATED CHRNA9 WILD-TYPE
  NO               4               90
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CHRNA9 MUTATED                                     4
  CHRNA9 WILD-TYPE                                 126
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CHRNA9 MUTATED                                       0
  CHRNA9 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CHRNA9 MUTATED                                                  0
  CHRNA9 WILD-TYPE                                                2
D72V9, 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                           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D72V10, continuous
D72V11, continuous
[1] "Remove cluster labels:" "CHRNA9 MUTATED"        
clus
  CHRNA9 MUTATED CHRNA9 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"CHRNA9 WILD-TYPE" "CHRNA9 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CHRNA9 MUTATED    1  2  0  1
  CHRNA9 WILD-TYPE 78 48  4  2
D72V12, multiclass
    clus
vv   CHRNA9 MUTATED CHRNA9 WILD-TYPE
  R0              1               78
  R1              2               48
  R2              0                4
  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"
D72V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHRNA9 MUTATED       0                         0     4
  CHRNA9 WILD-TYPE     9                         5   124
D72V14, multiclass
                           clus
vv                          CHRNA9 MUTATED CHRNA9 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                  cls
clus                 0   1
  CHRNA9 MUTATED     0   2
  CHRNA9 WILD-TYPE   5 103
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA9 MUTATED      0    2
  CHRNA9 WILD-TYPE    5  103
                        clus
vv                       CHRNA9 MUTATED CHRNA9 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2              103
[1] 2 2
[1] FALSE

Clustering(73) Variable = KLHL20 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2               0  1
  KLHL20 MUTATED    0  3
  KLHL20 WILD-TYPE 68 73
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               3              141 
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               3               73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  KLHL20 MUTATED KLHL20 WILD-TYPE 
            3.62             0.03 
  KLHL20 MUTATED KLHL20 WILD-TYPE 
           20.19            75.12 
  KLHL20 MUTATED KLHL20 WILD-TYPE 
           19.82            14.17 
[1] "3.6 - 20.2 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "2"  
D73V2, 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        3        8        23       100         4        4
D73V3, multiclass
           clus
vv          KLHL20 MUTATED KLHL20 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   122
D73V4, multiclass
       clus
vv      KLHL20 MUTATED KLHL20 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D73V5, binary
                  cls
clus                 0   1
  KLHL20 MUTATED     0   3
  KLHL20 WILD-TYPE  37 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL20 MUTATED      0    3
  KLHL20 WILD-TYPE   37  105
   clus
vv  KLHL20 MUTATED KLHL20 WILD-TYPE
  0              0               37
  1              3              105
[1] 2 2
[1] FALSE
D73V6, binary
                  cls
clus                0  1
  KLHL20 MUTATED    2  0
  KLHL20 WILD-TYPE 64  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL20 MUTATED      2    0
  KLHL20 WILD-TYPE   64    4
   clus
vv  KLHL20 MUTATED KLHL20 WILD-TYPE
  0              2               64
  1              0                4
[1] 2 2
[1] FALSE
D73V7, binary
                  cls
clus                0  1
  KLHL20 MUTATED    2  1
  KLHL20 WILD-TYPE 65 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL20 MUTATED      2    1
  KLHL20 WILD-TYPE   65   78
        clus
vv       KLHL20 MUTATED KLHL20 WILD-TYPE
  FEMALE              2               65
  MALE                1               78
[1] 2 2
[1] FALSE
D73V8, binary
                  cls
clus                0  1
  KLHL20 MUTATED    3  0
  KLHL20 WILD-TYPE 91 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL20 MUTATED      3    0
  KLHL20 WILD-TYPE   91   36
     clus
vv    KLHL20 MUTATED KLHL20 WILD-TYPE
  NO               3               91
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KLHL20 MUTATED                                     3
  KLHL20 WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KLHL20 MUTATED                                       0
  KLHL20 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KLHL20 MUTATED                                                  0
  KLHL20 WILD-TYPE                                                2
D73V9, 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                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D73V10, continuous
[1] "Remove cluster labels:" "KLHL20 MUTATED"        
clus
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               2               48 
      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-HV-AA8V       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-IB-AAUU       TCGA-LB-A7SX 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
D73V11, continuous
[1] "Remove cluster labels:" "KLHL20 MUTATED"        
clus
  KLHL20 MUTATED KLHL20 WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" "KLHL20 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  KLHL20 MUTATED    2  1  0  0
  KLHL20 WILD-TYPE 77 49  4  3
D73V12, multiclass
    clus
vv   KLHL20 MUTATED KLHL20 WILD-TYPE
  R0              2               77
  R1              1               49
  R2              0                4
  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"
D73V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLHL20 MUTATED       0                         0     3
  KLHL20 WILD-TYPE     9                         5   125
D73V14, multiclass
                           clus
vv                          KLHL20 MUTATED KLHL20 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                  cls
clus                 0   1
  KLHL20 MUTATED     0   3
  KLHL20 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL20 MUTATED      0    3
  KLHL20 WILD-TYPE    5  102
                        clus
vv                       KLHL20 MUTATED KLHL20 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(74) Variable = NUP210L MUTATION ANALYSIS
D74V1, survival
                   sevent
clus2                0  1
  NUP210L MUTATED    3  2
  NUP210L WILD-TYPE 65 74
  NUP210L MUTATED NUP210L WILD-TYPE 
                5               139 
  NUP210L MUTATED NUP210L WILD-TYPE 
                2                74 
$`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        39.98 

$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        15.12        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        24.23        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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  NUP210L MUTATED NUP210L WILD-TYPE 
            15.35              0.03 
  NUP210L MUTATED NUP210L WILD-TYPE 
            41.33             75.12 
  NUP210L MUTATED NUP210L WILD-TYPE 
            20.88             13.84 
[1] "15.3 - 41.3 (20.9)" "0.0 - 75.1 (13.8)" 
[1] "hr=" "2.3"
D74V2, 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        3        8        22        99         4        4
D74V3, multiclass
           clus
vv          NUP210L MUTATED NUP210L WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               1                22
  STAGE IIB               4                99
  STAGE III               0                 4
  STAGE IV                0                 4
[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   4  16   120
D74V4, multiclass
       clus
vv      NUP210L MUTATED NUP210L WILD-TYPE
  T1                  0                 4
  T2                  0                16
  T3+T4               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"
D74V5, binary
                   cls
clus                  0   1
  NUP210L MUTATED     1   4
  NUP210L WILD-TYPE  36 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED      1    4
  NUP210L WILD-TYPE   36  104
   clus
vv  NUP210L MUTATED NUP210L WILD-TYPE
  0               1                36
  1               4               104
[1] 2 2
[1] FALSE
D74V6, binary
                   cls
clus                 0  1
  NUP210L MUTATED    4  0
  NUP210L WILD-TYPE 62  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED      4    0
  NUP210L WILD-TYPE   62    4
   clus
vv  NUP210L MUTATED NUP210L WILD-TYPE
  0               4                62
  1               0                 4
[1] 2 2
[1] FALSE
D74V7, binary
                   cls
clus                 0  1
  NUP210L MUTATED    4  1
  NUP210L WILD-TYPE 63 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED      4    1
  NUP210L WILD-TYPE   63   78
        clus
vv       NUP210L MUTATED NUP210L WILD-TYPE
  FEMALE               4                63
  MALE                 1                78
[1] 2 2
[1] FALSE
D74V8, binary
                   cls
clus                 0  1
  NUP210L MUTATED    5  0
  NUP210L WILD-TYPE 89 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED      5    0
  NUP210L WILD-TYPE   89   36
     clus
vv    NUP210L MUTATED NUP210L WILD-TYPE
  NO                5                89
  YES               0                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NUP210L MUTATED                                     4
  NUP210L WILD-TYPE                                 126
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NUP210L MUTATED                                       0
  NUP210L WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NUP210L MUTATED                                                  1
  NUP210L WILD-TYPE                                                1
D74V9, 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                            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D74V10, continuous
D74V11, continuous
                   vv
clus                R0 R1 R2 RX
  NUP210L MUTATED    4  1  0  0
  NUP210L WILD-TYPE 75 49  4  3
D74V12, multiclass
    clus
vv   NUP210L MUTATED NUP210L WILD-TYPE
  R0               4                75
  R1               1                49
  R2               0                 4
  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"
D74V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUP210L MUTATED       0                         0     4
  NUP210L WILD-TYPE     9                         5   124
D74V14, multiclass
                           clus
vv                          NUP210L MUTATED NUP210L WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                   cls
clus                  0   1
  NUP210L MUTATED     0   4
  NUP210L WILD-TYPE   5 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED      0    4
  NUP210L WILD-TYPE    5  101
                        clus
vv                       NUP210L MUTATED NUP210L WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4               101
[1] 2 2
[1] FALSE

Clustering(75) Variable = AQP7 MUTATION ANALYSIS
D75V1, survival
                sevent
clus2             0  1
  AQP7 MUTATED    4  2
  AQP7 WILD-TYPE 64 74
  AQP7 MUTATED AQP7 WILD-TYPE 
             6            138 
  AQP7 MUTATED AQP7 WILD-TYPE 
             2             74 
$`AQP7 MUTATED`
TCGA-3A-A9IH TCGA-3A-A9IZ TCGA-FB-A545 TCGA-H6-8124 TCGA-IB-7651 TCGA-YB-A89D 
       33.57        10.13        12.66        12.89        19.82        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        42.31        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        58.98        43.50        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        24.43        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 
       16.37         0.03         7.50        12.53        34.82        23.54 
TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-A45N TCGA-HV-A5A3 
       15.55         4.04         5.03         1.02        13.84         4.21 
TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X 
        7.63         9.50        66.94         8.28        30.25        17.49 
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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       16.37        31.27        23.67        12.76        66.28        15.35 

  AQP7 MUTATED AQP7 WILD-TYPE 
         10.13           0.03 
  AQP7 MUTATED AQP7 WILD-TYPE 
         33.57          75.12 
  AQP7 MUTATED AQP7 WILD-TYPE 
        12.775         14.435 
[1] "10.1 - 33.6 (12.8)" "0.0 - 75.1 (14.4)" 
[1] "hr=" "1.5"
D75V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AQP7 MUTATED          1        0         0         5         0        0
  AQP7 WILD-TYPE        2        8        23        98         4        4
D75V3, multiclass
           clus
vv          AQP7 MUTATED AQP7 WILD-TYPE
  STAGE IA             1              2
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            5             98
  STAGE III            0              4
  STAGE IV             0              4
[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     5
  AQP7 WILD-TYPE   3  16   120
D75V4, multiclass
       clus
vv      AQP7 MUTATED AQP7 WILD-TYPE
  T1               1              3
  T2               0             16
  T3+T4            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"
D75V5, binary
                cls
clus               0   1
  AQP7 MUTATED     1   5
  AQP7 WILD-TYPE  36 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      1    5
  AQP7 WILD-TYPE   36  103
   clus
vv  AQP7 MUTATED AQP7 WILD-TYPE
  0            1             36
  1            5            103
[1] 2 2
[1] FALSE
D75V6, binary
                cls
clus              0  1
  AQP7 MUTATED    3  0
  AQP7 WILD-TYPE 63  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      3    0
  AQP7 WILD-TYPE   63    4
   clus
vv  AQP7 MUTATED AQP7 WILD-TYPE
  0            3             63
  1            0              4
[1] 2 2
[1] FALSE
D75V7, binary
                cls
clus              0  1
  AQP7 MUTATED    4  2
  AQP7 WILD-TYPE 63 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      4    2
  AQP7 WILD-TYPE   63   77
        clus
vv       AQP7 MUTATED AQP7 WILD-TYPE
  FEMALE            4             63
  MALE              2             77
[1] 2 2
[1] FALSE
D75V8, binary
                cls
clus              0  1
  AQP7 MUTATED    3  3
  AQP7 WILD-TYPE 91 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      3    3
  AQP7 WILD-TYPE   91   33
     clus
vv    AQP7 MUTATED AQP7 WILD-TYPE
  NO             3             91
  YES            3             33
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AQP7 MUTATED                                     6
  AQP7 WILD-TYPE                                 124
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AQP7 MUTATED                                       0
  AQP7 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AQP7 MUTATED                                                  0
  AQP7 WILD-TYPE                                                2
D75V9, multiclass
                                                  clus
vv                                                 AQP7 MUTATED AQP7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         6            124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D75V10, continuous
[1] "Remove cluster labels:" "AQP7 MUTATED"          
clus
  AQP7 MUTATED AQP7 WILD-TYPE 
             2             48 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-A45N     TCGA-HV-AA8V 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
D75V11, continuous
[1] "Remove cluster labels:" "AQP7 MUTATED"          
clus
  AQP7 MUTATED AQP7 WILD-TYPE 
             2             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7891 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"AQP7 WILD-TYPE" "AQP7 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  AQP7 MUTATED    4  1  0  0
  AQP7 WILD-TYPE 75 49  4  3
D75V12, multiclass
    clus
vv   AQP7 MUTATED AQP7 WILD-TYPE
  R0            4             75
  R1            1             49
  R2            0              4
  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"
D75V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AQP7 MUTATED       0                         0     6
  AQP7 WILD-TYPE     9                         5   122
D75V14, multiclass
                           clus
vv                          AQP7 MUTATED AQP7 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            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"
D75V15, binary
                cls
clus               0   1
  AQP7 MUTATED     1   5
  AQP7 WILD-TYPE   4 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  AQP7 MUTATED      1    5
  AQP7 WILD-TYPE    4  100
                        clus
vv                       AQP7 MUTATED AQP7 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            5            100
[1] 2 2
[1] FALSE

Clustering(76) Variable = P2RY1 MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2              0  1
  P2RY1 MUTATED    2  3
  P2RY1 WILD-TYPE 66 73
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              5             139 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
              3              73 
$`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        16.37 

$`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        42.31        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        58.98        43.50        20.84        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  P2RY1 MUTATED P2RY1 WILD-TYPE 
           7.36            0.03 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
          19.82           75.12 
  P2RY1 MUTATED P2RY1 WILD-TYPE 
          16.37           14.17 
[1] "7.4 - 19.8 (16.4)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.4"
D76V2, 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        3        8        20       101         4        4
D76V3, multiclass
           clus
vv          P2RY1 MUTATED P2RY1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             3              20
  STAGE IIB             2             101
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   120
D76V4, multiclass
       clus
vv      P2RY1 MUTATED P2RY1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D76V5, binary
                 cls
clus                0   1
  P2RY1 MUTATED     3   2
  P2RY1 WILD-TYPE  34 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      3    2
  P2RY1 WILD-TYPE   34  106
   clus
vv  P2RY1 MUTATED P2RY1 WILD-TYPE
  0             3              34
  1             2             106
[1] 2 2
[1] FALSE
D76V6, binary
                 cls
clus               0  1
  P2RY1 MUTATED    3  0
  P2RY1 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      3    0
  P2RY1 WILD-TYPE   63    4
   clus
vv  P2RY1 MUTATED P2RY1 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D76V7, binary
                 cls
clus               0  1
  P2RY1 MUTATED    2  3
  P2RY1 WILD-TYPE 65 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      2    3
  P2RY1 WILD-TYPE   65   76
        clus
vv       P2RY1 MUTATED P2RY1 WILD-TYPE
  FEMALE             2              65
  MALE               3              76
[1] 2 2
[1] FALSE
D76V8, binary
                 cls
clus               0  1
  P2RY1 MUTATED    4  1
  P2RY1 WILD-TYPE 90 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      4    1
  P2RY1 WILD-TYPE   90   35
     clus
vv    P2RY1 MUTATED P2RY1 WILD-TYPE
  NO              4              90
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  P2RY1 MUTATED                                     5
  P2RY1 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  P2RY1 MUTATED                                       0
  P2RY1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  P2RY1 MUTATED                                                  0
  P2RY1 WILD-TYPE                                                2
D76V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D76V10, continuous
D76V11, continuous
                 vv
clus              R0 R1 R2 RX
  P2RY1 MUTATED    4  1  0  0
  P2RY1 WILD-TYPE 75 49  4  3
D76V12, multiclass
    clus
vv   P2RY1 MUTATED P2RY1 WILD-TYPE
  R0             4              75
  R1             1              49
  R2             0               4
  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"
D76V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  P2RY1 MUTATED       0                         0     5
  P2RY1 WILD-TYPE     9                         5   123
D76V14, multiclass
                           clus
vv                          P2RY1 MUTATED P2RY1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D76V15, binary
                 cls
clus                0   1
  P2RY1 MUTATED     0   5
  P2RY1 WILD-TYPE   5 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RY1 MUTATED      0    5
  P2RY1 WILD-TYPE    5  100
                        clus
vv                       P2RY1 MUTATED P2RY1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             100
[1] 2 2
[1] FALSE

Clustering(77) Variable = CCDC33 MUTATION ANALYSIS
D77V1, survival
                  sevent
clus2               0  1
  CCDC33 MUTATED    0  3
  CCDC33 WILD-TYPE 68 73
  CCDC33 MUTATED CCDC33 WILD-TYPE 
               3              141 
  CCDC33 MUTATED CCDC33 WILD-TYPE 
               3               73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  CCDC33 MUTATED CCDC33 WILD-TYPE 
            3.95             0.03 
  CCDC33 MUTATED CCDC33 WILD-TYPE 
           17.03            75.12 
  CCDC33 MUTATED CCDC33 WILD-TYPE 
           10.98            14.40 
[1] "4.0 - 17.0 (11.0)" "0.0 - 75.1 (14.4)"
[1] "hr=" "3.3"
D77V2, 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        3        8        23       100         4        4
D77V3, multiclass
           clus
vv          CCDC33 MUTATED CCDC33 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   122
D77V4, multiclass
       clus
vv      CCDC33 MUTATED CCDC33 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D77V5, binary
                  cls
clus                 0   1
  CCDC33 MUTATED     0   3
  CCDC33 WILD-TYPE  37 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC33 MUTATED      0    3
  CCDC33 WILD-TYPE   37  105
   clus
vv  CCDC33 MUTATED CCDC33 WILD-TYPE
  0              0               37
  1              3              105
[1] 2 2
[1] FALSE
D77V6, binary
                  cls
clus                0  1
  CCDC33 MUTATED    1  0
  CCDC33 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC33 MUTATED      1    0
  CCDC33 WILD-TYPE   65    4
   clus
vv  CCDC33 MUTATED CCDC33 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D77V7, binary
                  cls
clus                0  1
  CCDC33 MUTATED    0  3
  CCDC33 WILD-TYPE 67 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC33 MUTATED      0    3
  CCDC33 WILD-TYPE   67   76
        clus
vv       CCDC33 MUTATED CCDC33 WILD-TYPE
  FEMALE              0               67
  MALE                3               76
[1] 2 2
[1] FALSE
D77V8, binary
                  cls
clus                0  1
  CCDC33 MUTATED    2  0
  CCDC33 WILD-TYPE 92 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC33 MUTATED      2    0
  CCDC33 WILD-TYPE   92   36
     clus
vv    CCDC33 MUTATED CCDC33 WILD-TYPE
  NO               2               92
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC33 MUTATED                                     2
  CCDC33 WILD-TYPE                                 128
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC33 MUTATED                                       1
  CCDC33 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC33 MUTATED                                                  0
  CCDC33 WILD-TYPE                                                2
D77V9, 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                           128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D77V10, continuous
D77V11, continuous
                  vv
clus               R0 R1 R2 RX
  CCDC33 MUTATED    1  1  0  1
  CCDC33 WILD-TYPE 78 49  4  2
D77V12, multiclass
    clus
vv   CCDC33 MUTATED CCDC33 WILD-TYPE
  R0              1               78
  R1              1               49
  R2              0                4
  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"
D77V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC33 MUTATED       0                         1     2
  CCDC33 WILD-TYPE     9                         4   126
D77V14, multiclass
                           clus
vv                          CCDC33 MUTATED CCDC33 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  2              126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, binary
                  cls
clus                 0   1
  CCDC33 MUTATED     0   2
  CCDC33 WILD-TYPE   5 103
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC33 MUTATED      0    2
  CCDC33 WILD-TYPE    5  103
                        clus
vv                       CCDC33 MUTATED CCDC33 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2              103
[1] 2 2
[1] FALSE

Clustering(78) Variable = WRN MUTATION ANALYSIS
D78V1, survival
               sevent
clus2            0  1
  WRN MUTATED    1  3
  WRN WILD-TYPE 67 73
  WRN MUTATED WRN WILD-TYPE 
            4           140 
  WRN MUTATED WRN WILD-TYPE 
            3            73 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-AAUS TCGA-IB-AAUT TCGA-IB-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
        6.02         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  WRN MUTATED WRN WILD-TYPE 
         4.04          0.03 
  WRN MUTATED WRN WILD-TYPE 
        19.96         75.12 
  WRN MUTATED WRN WILD-TYPE 
       11.570        14.435 
[1] "4.0 - 20.0 (11.6)" "0.0 - 75.1 (14.4)"
[1] "hr=" "2.2"
D78V2, 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        3        8        23        99         4        4
D78V3, multiclass
           clus
vv          WRN MUTATED WRN WILD-TYPE
  STAGE IA            0             3
  STAGE IB            0             8
  STAGE IIA           0            23
  STAGE IIB           4            99
  STAGE III           0             4
  STAGE IV            0             4
[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   4  16   121
D78V4, multiclass
       clus
vv      WRN MUTATED WRN WILD-TYPE
  T1              0             4
  T2              0            16
  T3+T4           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"
D78V5, binary
               cls
clus              0   1
  WRN MUTATED     0   4
  WRN WILD-TYPE  37 104
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      0    4
  WRN WILD-TYPE   37  104
   clus
vv  WRN MUTATED WRN WILD-TYPE
  0           0            37
  1           4           104
[1] 2 2
[1] FALSE
D78V6, binary
               cls
clus             0  1
  WRN MUTATED    2  0
  WRN WILD-TYPE 64  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      2    0
  WRN WILD-TYPE   64    4
   clus
vv  WRN MUTATED WRN WILD-TYPE
  0           2            64
  1           0             4
[1] 2 2
[1] FALSE
D78V7, binary
               cls
clus             0  1
  WRN MUTATED    0  4
  WRN WILD-TYPE 67 75
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      0    4
  WRN WILD-TYPE   67   75
        clus
vv       WRN MUTATED WRN WILD-TYPE
  FEMALE           0            67
  MALE             4            75
[1] 2 2
[1] FALSE
D78V8, binary
               cls
clus             0  1
  WRN MUTATED    4  0
  WRN WILD-TYPE 90 36
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      4    0
  WRN WILD-TYPE   90   36
     clus
vv    WRN MUTATED WRN WILD-TYPE
  NO            4            90
  YES           0            36
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WRN MUTATED                                     4
  WRN WILD-TYPE                                 126
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WRN MUTATED                                       0
  WRN WILD-TYPE                                    13
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WRN MUTATED                                                  0
  WRN WILD-TYPE                                                2
D78V9, multiclass
                                                  clus
vv                                                 WRN MUTATED WRN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            13
  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"
D78V10, continuous
[1] "Remove cluster labels:" "WRN MUTATED"           
clus
  WRN MUTATED WRN WILD-TYPE 
            1            49 
   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-HV-AA8V 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-HZ-A8P1    TCGA-IB-7644    TCGA-IB-7649 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-IB-7651    TCGA-IB-7885    TCGA-IB-7886    TCGA-IB-7887    TCGA-IB-7891 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-8127    TCGA-IB-A5SS    TCGA-IB-A6UF    TCGA-IB-A6UG 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUS    TCGA-IB-AAUT    TCGA-IB-AAUU 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-LB-A7SX    TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-S4-A8RM    TCGA-S4-A8RP 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
   TCGA-US-A774    TCGA-XD-AAUL    TCGA-XN-A8T5    TCGA-YY-A8LH 
"WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" "WRN WILD-TYPE" 
D78V11, continuous
               vv
clus            R0 R1 R2 RX
  WRN MUTATED    1  3  0  0
  WRN WILD-TYPE 78 47  4  3
D78V12, multiclass
    clus
vv   WRN MUTATED WRN WILD-TYPE
  R0           1            78
  R1           3            47
  R2           0             4
  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"
D78V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WRN MUTATED       0                         0     4
  WRN WILD-TYPE     9                         5   124
D78V14, multiclass
                           clus
vv                          WRN MUTATED WRN WILD-TYPE
  ASIAN                               0             9
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, binary
               cls
clus              0   1
  WRN MUTATED     0   3
  WRN WILD-TYPE   5 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  WRN MUTATED      0    3
  WRN WILD-TYPE    5  102
                        clus
vv                       WRN MUTATED WRN WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           3           102
[1] 2 2
[1] FALSE

Clustering(79) Variable = C1ORF125 MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  C1ORF125 MUTATED    1  3
  C1ORF125 WILD-TYPE 67 73
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
                 4                140 
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
                 3                 73 
$`C1ORF125 MUTATED`
TCGA-HZ-8636 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 
       17.92        15.35        19.82        41.33 

$`C1ORF125 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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
        9.83        12.43        14.93        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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 
       19.82        12.95        49.38         4.77        21.90        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
             15.35               0.03 
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
             41.33              75.12 
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
             18.87              13.99 
[1] "15.3 - 41.3 (18.9)" "0.0 - 75.1 (14.0)" 
[1] "hr=" "1"  
D79V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  C1ORF125 MUTATED          0        0         0         3         0        1
  C1ORF125 WILD-TYPE        3        8        23       100         4        3
D79V3, multiclass
           clus
vv          C1ORF125 MUTATED C1ORF125 WILD-TYPE
  STAGE IA                 0                  3
  STAGE IB                 0                  8
  STAGE IIA                0                 23
  STAGE IIB                3                100
  STAGE III                0                  4
  STAGE IV                 1                  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
  C1ORF125 MUTATED     0   0     4
  C1ORF125 WILD-TYPE   4  16   121
D79V4, multiclass
       clus
vv      C1ORF125 MUTATED C1ORF125 WILD-TYPE
  T1                   0                  4
  T2                   0                 16
  T3+T4                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"
D79V5, binary
                    cls
clus                   0   1
  C1ORF125 MUTATED     1   3
  C1ORF125 WILD-TYPE  36 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED      1    3
  C1ORF125 WILD-TYPE   36  105
   clus
vv  C1ORF125 MUTATED C1ORF125 WILD-TYPE
  0                1                 36
  1                3                105
[1] 2 2
[1] FALSE
D79V6, binary
                    cls
clus                  0  1
  C1ORF125 MUTATED    3  1
  C1ORF125 WILD-TYPE 63  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED      3    1
  C1ORF125 WILD-TYPE   63    3
   clus
vv  C1ORF125 MUTATED C1ORF125 WILD-TYPE
  0                3                 63
  1                1                  3
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                  0  1
  C1ORF125 MUTATED    4  0
  C1ORF125 WILD-TYPE 63 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED      4    0
  C1ORF125 WILD-TYPE   63   79
        clus
vv       C1ORF125 MUTATED C1ORF125 WILD-TYPE
  FEMALE                4                 63
  MALE                  0                 79
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                  0  1
  C1ORF125 MUTATED    3  0
  C1ORF125 WILD-TYPE 91 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED      3    0
  C1ORF125 WILD-TYPE   91   36
     clus
vv    C1ORF125 MUTATED C1ORF125 WILD-TYPE
  NO                 3                 91
  YES                0                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C1ORF125 MUTATED                                     4
  C1ORF125 WILD-TYPE                                 126
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C1ORF125 MUTATED                                       0
  C1ORF125 WILD-TYPE                                    13
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C1ORF125 MUTATED                                                  0
  C1ORF125 WILD-TYPE                                                2
D79V9, multiclass
                                                  clus
vv                                                 C1ORF125 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 C1ORF125 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            13
  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"
D79V10, continuous
D79V11, continuous
                    vv
clus                 R0 R1 R2 RX
  C1ORF125 MUTATED    2  2  0  0
  C1ORF125 WILD-TYPE 77 48  4  3
D79V12, multiclass
    clus
vv   C1ORF125 MUTATED C1ORF125 WILD-TYPE
  R0                2                 77
  R1                2                 48
  R2                0                  4
  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"
D79V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C1ORF125 MUTATED       0                         0     3
  C1ORF125 WILD-TYPE     9                         5   125
D79V14, multiclass
                           clus
vv                          C1ORF125 MUTATED C1ORF125 WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    3                125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, binary
                    cls
clus                   0   1
  C1ORF125 MUTATED     0   3
  C1ORF125 WILD-TYPE   5 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED      0    3
  C1ORF125 WILD-TYPE    5  102
                        clus
vv                       C1ORF125 MUTATED C1ORF125 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                3                102
[1] 2 2
[1] FALSE

Clustering(80) Variable = SIGLEC14 MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                 0  1
  SIGLEC14 MUTATED    0  4
  SIGLEC14 WILD-TYPE 68 72
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 4                140 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 4                 72 
$`SIGLEC14 MUTATED`
TCGA-2J-AAB1 TCGA-2J-AAB6 TCGA-HZ-8317 TCGA-IB-7651 
        2.17         9.63        12.43        19.82 

$`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 
       42.31        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
              2.17               0.03 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
             19.82              75.12 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
            11.030             14.435 
[1] "2.2 - 19.8 (11.0)" "0.0 - 75.1 (14.4)"
[1] "hr=" "3.2"
D80V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SIGLEC14 MUTATED          0        0         1         3         0        0
  SIGLEC14 WILD-TYPE        3        8        22       100         4        4
D80V3, multiclass
           clus
vv          SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  STAGE IA                 0                  3
  STAGE IB                 0                  8
  STAGE IIA                1                 22
  STAGE IIB                3                100
  STAGE III                0                  4
  STAGE IV                 0                  4
[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     4
  SIGLEC14 WILD-TYPE   4  16   121
D80V4, multiclass
       clus
vv      SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  T1                   0                  4
  T2                   0                 16
  T3+T4                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"
D80V5, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     1   3
  SIGLEC14 WILD-TYPE  36 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      1    3
  SIGLEC14 WILD-TYPE   36  105
   clus
vv  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  0                1                 36
  1                3                105
[1] 2 2
[1] FALSE
D80V6, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    3  0
  SIGLEC14 WILD-TYPE 63  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      3    0
  SIGLEC14 WILD-TYPE   63    4
   clus
vv  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  0                3                 63
  1                0                  4
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    2  2
  SIGLEC14 WILD-TYPE 65 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      2    2
  SIGLEC14 WILD-TYPE   65   77
        clus
vv       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  FEMALE                2                 65
  MALE                  2                 77
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                  0  1
  SIGLEC14 MUTATED    3  1
  SIGLEC14 WILD-TYPE 91 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      3    1
  SIGLEC14 WILD-TYPE   91   35
     clus
vv    SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  NO                 3                 91
  YES                1                 35
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SIGLEC14 MUTATED                                     3
  SIGLEC14 WILD-TYPE                                 127
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SIGLEC14 MUTATED                                       1
  SIGLEC14 WILD-TYPE                                    12
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SIGLEC14 MUTATED                                                  0
  SIGLEC14 WILD-TYPE                                                2
D80V9, multiclass
                                                  clus
vv                                                 SIGLEC14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 SIGLEC14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            12
  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"
D80V10, continuous
[1] "Remove cluster labels:" "SIGLEC14 MUTATED"      
clus
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 2                 48 
        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-HV-AA8V         TCGA-HZ-A77Q 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-7649         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-XN-A8T5         TCGA-YY-A8LH 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
D80V11, continuous
[1] "Remove cluster labels:" "SIGLEC14 MUTATED"      
clus
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 2                 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-7885 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-IB-7886         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-LB-A7SX 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUI         TCGA-XD-AAUL 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"SIGLEC14 WILD-TYPE" "SIGLEC14 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  SIGLEC14 MUTATED    3  1  0  0
  SIGLEC14 WILD-TYPE 76 49  4  3
D80V12, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  R0                3                 76
  R1                1                 49
  R2                0                  4
  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"
D80V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SIGLEC14 MUTATED       0                         0     4
  SIGLEC14 WILD-TYPE     9                         5   124
D80V14, multiclass
                           clus
vv                          SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V15, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     0   2
  SIGLEC14 WILD-TYPE   5 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      0    2
  SIGLEC14 WILD-TYPE    5  103
                        clus
vv                       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                2                103
[1] 2 2
[1] FALSE

Clustering(81) Variable = KRT2 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2             0  1
  KRT2 MUTATED    1  4
  KRT2 WILD-TYPE 67 72
  KRT2 MUTATED KRT2 WILD-TYPE 
             5            139 
  KRT2 MUTATED KRT2 WILD-TYPE 
             4             72 
$`KRT2 MUTATED`
TCGA-FB-AAPY TCGA-FB-AAQ3 TCGA-H6-8124 TCGA-HZ-8003 TCGA-IB-7651 
       34.82         1.02        12.89        19.59        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        19.50         0.13        20.19        17.03        23.21 
TCGA-HZ-8002 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
       12.03         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  KRT2 MUTATED KRT2 WILD-TYPE 
          1.02           0.03 
  KRT2 MUTATED KRT2 WILD-TYPE 
         34.82          75.12 
  KRT2 MUTATED KRT2 WILD-TYPE 
         19.59          14.17 
[1] "1.0 - 34.8 (19.6)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.4"
D81V2, 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        3        8        23        98         4        4
D81V3, multiclass
           clus
vv          KRT2 MUTATED KRT2 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            5             98
  STAGE III            0              4
  STAGE IV             0              4
[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   4  15   121
D81V4, multiclass
       clus
vv      KRT2 MUTATED KRT2 WILD-TYPE
  T1               0              4
  T2               1             15
  T3+T4            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"
D81V5, binary
                cls
clus               0   1
  KRT2 MUTATED     0   5
  KRT2 WILD-TYPE  37 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      0    5
  KRT2 WILD-TYPE   37  103
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0            0             37
  1            5            103
[1] 2 2
[1] FALSE
D81V6, binary
                cls
clus              0  1
  KRT2 MUTATED    2  0
  KRT2 WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      2    0
  KRT2 WILD-TYPE   64    4
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D81V7, binary
                cls
clus              0  1
  KRT2 MUTATED    4  1
  KRT2 WILD-TYPE 63 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      4    1
  KRT2 WILD-TYPE   63   78
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  FEMALE            4             63
  MALE              1             78
[1] 2 2
[1] FALSE
D81V8, binary
                cls
clus              0  1
  KRT2 MUTATED    3  2
  KRT2 WILD-TYPE 91 34
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      3    2
  KRT2 WILD-TYPE   91   34
     clus
vv    KRT2 MUTATED KRT2 WILD-TYPE
  NO             3             91
  YES            2             34
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KRT2 MUTATED                                     5
  KRT2 WILD-TYPE                                 125
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KRT2 MUTATED                                       0
  KRT2 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KRT2 MUTATED                                                  0
  KRT2 WILD-TYPE                                                2
D81V9, multiclass
                                                  clus
vv                                                 KRT2 MUTATED KRT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D81V10, continuous
D81V11, continuous
                vv
clus             R0 R1 R2 RX
  KRT2 MUTATED    5  0  0  0
  KRT2 WILD-TYPE 74 50  4  3
D81V12, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  R0            5             74
  R1            0             50
  R2            0              4
  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"
D81V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRT2 MUTATED       0                         0     5
  KRT2 WILD-TYPE     9                         5   123
D81V14, multiclass
                           clus
vv                          KRT2 MUTATED KRT2 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            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"
D81V15, binary
                cls
clus               0   1
  KRT2 MUTATED     0   5
  KRT2 WILD-TYPE   5 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      0    5
  KRT2 WILD-TYPE    5  100
                        clus
vv                       KRT2 MUTATED KRT2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5            100
[1] 2 2
[1] FALSE

Clustering(82) Variable = MSH2 MUTATION ANALYSIS
D82V1, survival
                sevent
clus2             0  1
  MSH2 MUTATED    1  3
  MSH2 WILD-TYPE 67 73
  MSH2 MUTATED MSH2 WILD-TYPE 
             4            140 
  MSH2 MUTATED MSH2 WILD-TYPE 
             3             73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       20.19        17.03        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  MSH2 MUTATED MSH2 WILD-TYPE 
          3.62           0.03 
  MSH2 MUTATED MSH2 WILD-TYPE 
         23.21          75.12 
  MSH2 MUTATED MSH2 WILD-TYPE 
        15.925         14.285 
[1] "3.6 - 23.2 (15.9)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.4"
D82V2, 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        3        8        23       100         3        4
D82V3, multiclass
           clus
vv          MSH2 MUTATED MSH2 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            3            100
  STAGE III            1              3
  STAGE IV             0              4
[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   4  16   121
D82V4, multiclass
       clus
vv      MSH2 MUTATED MSH2 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D82V5, binary
                cls
clus               0   1
  MSH2 MUTATED     1   3
  MSH2 WILD-TYPE  36 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      1    3
  MSH2 WILD-TYPE   36  105
   clus
vv  MSH2 MUTATED MSH2 WILD-TYPE
  0            1             36
  1            3            105
[1] 2 2
[1] FALSE
D82V6, binary
                cls
clus              0  1
  MSH2 MUTATED    2  0
  MSH2 WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      2    0
  MSH2 WILD-TYPE   64    4
   clus
vv  MSH2 MUTATED MSH2 WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D82V7, binary
                cls
clus              0  1
  MSH2 MUTATED    2  2
  MSH2 WILD-TYPE 65 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      2    2
  MSH2 WILD-TYPE   65   77
        clus
vv       MSH2 MUTATED MSH2 WILD-TYPE
  FEMALE            2             65
  MALE              2             77
[1] 2 2
[1] FALSE
D82V8, binary
                cls
clus              0  1
  MSH2 MUTATED    4  0
  MSH2 WILD-TYPE 90 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      4    0
  MSH2 WILD-TYPE   90   36
     clus
vv    MSH2 MUTATED MSH2 WILD-TYPE
  NO             4             90
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MSH2 MUTATED                                     4
  MSH2 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MSH2 MUTATED                                       0
  MSH2 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MSH2 MUTATED                                                  0
  MSH2 WILD-TYPE                                                2
D82V9, multiclass
                                                  clus
vv                                                 MSH2 MUTATED MSH2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D82V10, continuous
[1] "Remove cluster labels:" "MSH2 MUTATED"          
clus
  MSH2 MUTATED MSH2 WILD-TYPE 
             2             48 
    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-HV-AA8V     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-IB-AAUU     TCGA-LB-A7SX 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
D82V11, continuous
[1] "Remove cluster labels:" "MSH2 MUTATED"          
clus
  MSH2 MUTATED MSH2 WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"MSH2 WILD-TYPE" "MSH2 WILD-TYPE" "MSH2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MSH2 MUTATED    3  1  0  0
  MSH2 WILD-TYPE 76 49  4  3
D82V12, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  R0            3             76
  R1            1             49
  R2            0              4
  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"
D82V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MSH2 MUTATED       0                         0     4
  MSH2 WILD-TYPE     9                         5   124
D82V14, multiclass
                           clus
vv                          MSH2 MUTATED MSH2 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V15, binary
                cls
clus               0   1
  MSH2 MUTATED     0   4
  MSH2 WILD-TYPE   5 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED      0    4
  MSH2 WILD-TYPE    5  101
                        clus
vv                       MSH2 MUTATED MSH2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(83) Variable = MORF4L1 MUTATION ANALYSIS
D83V1, survival
                   sevent
clus2                0  1
  MORF4L1 MUTATED    1  2
  MORF4L1 WILD-TYPE 67 74
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                3               141 
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                2                74 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 TCGA-IB-7889 
       19.82        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-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-Q3-A5QY 
       12.92        12.46        10.29        19.20         8.78        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
            12.95              0.03 
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
            41.33             75.12 
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
            15.45             14.17 
[1] "12.9 - 41.3 (15.4)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "1"  
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        3        8        23       101         3        4
D83V3, multiclass
           clus
vv          MORF4L1 MUTATED MORF4L1 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               0                23
  STAGE IIB               2               101
  STAGE III               1                 3
  STAGE IV                0                 4
[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   4  16   122
D83V4, multiclass
       clus
vv      MORF4L1 MUTATED MORF4L1 WILD-TYPE
  T1                  0                 4
  T2                  0                16
  T3+T4               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"
D83V5, binary
                   cls
clus                  0   1
  MORF4L1 MUTATED     1   2
  MORF4L1 WILD-TYPE  36 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MORF4L1 MUTATED      1    2
  MORF4L1 WILD-TYPE   36  106
   clus
vv  MORF4L1 MUTATED MORF4L1 WILD-TYPE
  0               1                36
  1               2               106
[1] 2 2
[1] FALSE
D83V6, binary
                   cls
clus                 0  1
  MORF4L1 MUTATED    1  0
  MORF4L1 WILD-TYPE 65  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MORF4L1 MUTATED      1    0
  MORF4L1 WILD-TYPE   65    4
   clus
vv  MORF4L1 MUTATED MORF4L1 WILD-TYPE
  0               1                65
  1               0                 4
[1] 2 2
[1] FALSE
D83V7, binary
                   cls
clus                 0  1
  MORF4L1 MUTATED    3  0
  MORF4L1 WILD-TYPE 64 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MORF4L1 MUTATED      3    0
  MORF4L1 WILD-TYPE   64   79
        clus
vv       MORF4L1 MUTATED MORF4L1 WILD-TYPE
  FEMALE               3                64
  MALE                 0                79
[1] 2 2
[1] FALSE
D83V8, binary
                   cls
clus                 0  1
  MORF4L1 MUTATED    2  1
  MORF4L1 WILD-TYPE 92 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MORF4L1 MUTATED      2    1
  MORF4L1 WILD-TYPE   92   35
     clus
vv    MORF4L1 MUTATED MORF4L1 WILD-TYPE
  NO                2                92
  YES               1                35
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MORF4L1 MUTATED                                     3
  MORF4L1 WILD-TYPE                                 127
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MORF4L1 MUTATED                                       0
  MORF4L1 WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MORF4L1 MUTATED                                                  0
  MORF4L1 WILD-TYPE                                                2
D83V9, 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                            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D83V10, continuous
[1] "Remove cluster labels:" "MORF4L1 MUTATED"       
clus
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                1                49 
       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-HV-AA8V        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-7887        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL        TCGA-XN-A8T5 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-YY-A8LH 
"MORF4L1 WILD-TYPE" 
D83V11, continuous
[1] "Remove cluster labels:" "MORF4L1 MUTATED"       
clus
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                1                39 
       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-XN-A8T5        TCGA-YY-A8LH 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  MORF4L1 MUTATED    1  1  0  0
  MORF4L1 WILD-TYPE 78 49  4  3
D83V12, multiclass
[1] "Remove cluster labels:" "MORF4L1 MUTATED"       
clus
  MORF4L1 MUTATED MORF4L1 WILD-TYPE 
                2               134 
       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-HV-A5A6        TCGA-HV-A7OL        TCGA-HV-AA8V 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-HV-AA8X        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-HZ-A9TJ        TCGA-IB-7644        TCGA-IB-7645        TCGA-IB-7646 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7647        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7652 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7888        TCGA-IB-7889 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-7890        TCGA-IB-7891        TCGA-IB-7893        TCGA-IB-7897 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SO        TCGA-IB-A5SP 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-A5SQ        TCGA-IB-A5SS        TCGA-IB-A5ST        TCGA-IB-A6UF 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-A6UG        TCGA-IB-A7LX        TCGA-IB-A7M4        TCGA-IB-AAUM 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-AAUN        TCGA-IB-AAUO        TCGA-IB-AAUP        TCGA-IB-AAUQ 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-IB-AAUR        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A8F3        TCGA-LB-A9Q5        TCGA-M8-A5N4 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-Q3-A5QY        TCGA-Q3-AA2A        TCGA-RB-A7B8 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-RB-AA9M        TCGA-S4-A8RM        TCGA-S4-A8RO        TCGA-S4-A8RP 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-US-A774        TCGA-US-A776        TCGA-US-A779        TCGA-US-A77E 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-US-A77G        TCGA-XD-AAUG        TCGA-XD-AAUH        TCGA-XD-AAUI 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-XD-AAUL        TCGA-XN-A8T3        TCGA-XN-A8T5        TCGA-YB-A89D 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
       TCGA-YY-A8LH        TCGA-Z5-AAPL 
"MORF4L1 WILD-TYPE" "MORF4L1 WILD-TYPE" 
D83V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MORF4L1 MUTATED       0                         0     3
  MORF4L1 WILD-TYPE     9                         5   125
D83V14, multiclass
                           clus
vv                          MORF4L1 MUTATED MORF4L1 WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V15, binary
                   cls
clus                  0   1
  MORF4L1 MUTATED     0   2
  MORF4L1 WILD-TYPE   5 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MORF4L1 MUTATED      0    2
  MORF4L1 WILD-TYPE    5  103
                        clus
vv                       MORF4L1 MUTATED MORF4L1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2               103
[1] 2 2
[1] FALSE

Clustering(84) Variable = KIAA0586 MUTATION ANALYSIS
D84V1, survival
                    sevent
clus2                 0  1
  KIAA0586 MUTATED    1  5
  KIAA0586 WILD-TYPE 67 71
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 6                138 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
                 5                 71 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       20.19        17.03        23.21        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 
       19.82        12.95        49.38         4.77        21.90        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-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-AAUO TCGA-IB-AAUP TCGA-IB-AAUQ TCGA-IB-AAUR TCGA-IB-AAUS 
        0.26         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 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
              3.62               0.03 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
             19.82              75.12 
  KIAA0586 MUTATED KIAA0586 WILD-TYPE 
            13.690             14.285 
[1] "3.6 - 19.8 (13.7)" "0.0 - 75.1 (14.3)"
[1] "hr=" "2.3"
D84V2, 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        3        7        23        98         4        4
D84V3, multiclass
           clus
vv          KIAA0586 MUTATED KIAA0586 WILD-TYPE
  STAGE IA                 0                  3
  STAGE IB                 1                  7
  STAGE IIA                0                 23
  STAGE IIB                5                 98
  STAGE III                0                  4
  STAGE IV                 0                  4
[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   4  15   120
D84V4, multiclass
       clus
vv      KIAA0586 MUTATED KIAA0586 WILD-TYPE
  T1                   0                  4
  T2                   1                 15
  T3+T4                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"
D84V5, binary
                    cls
clus                   0   1
  KIAA0586 MUTATED     1   5
  KIAA0586 WILD-TYPE  36 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      1    5
  KIAA0586 WILD-TYPE   36  103
   clus
vv  KIAA0586 MUTATED KIAA0586 WILD-TYPE
  0                1                 36
  1                5                103
[1] 2 2
[1] FALSE
D84V6, binary
                    cls
clus                  0  1
  KIAA0586 MUTATED    5  0
  KIAA0586 WILD-TYPE 61  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      5    0
  KIAA0586 WILD-TYPE   61    4
   clus
vv  KIAA0586 MUTATED KIAA0586 WILD-TYPE
  0                5                 61
  1                0                  4
[1] 2 2
[1] FALSE
D84V7, binary
                    cls
clus                  0  1
  KIAA0586 MUTATED    4  2
  KIAA0586 WILD-TYPE 63 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      4    2
  KIAA0586 WILD-TYPE   63   77
        clus
vv       KIAA0586 MUTATED KIAA0586 WILD-TYPE
  FEMALE                4                 63
  MALE                  2                 77
[1] 2 2
[1] FALSE
D84V8, binary
                    cls
clus                  0  1
  KIAA0586 MUTATED    6  0
  KIAA0586 WILD-TYPE 88 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      6    0
  KIAA0586 WILD-TYPE   88   36
     clus
vv    KIAA0586 MUTATED KIAA0586 WILD-TYPE
  NO                 6                 88
  YES                0                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA0586 MUTATED                                     6
  KIAA0586 WILD-TYPE                                 124
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA0586 MUTATED                                       0
  KIAA0586 WILD-TYPE                                    13
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA0586 MUTATED                                                  0
  KIAA0586 WILD-TYPE                                                2
D84V9, 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                             124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            13
  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"
D84V10, continuous
D84V11, continuous
                    vv
clus                 R0 R1 R2 RX
  KIAA0586 MUTATED    2  4  0  0
  KIAA0586 WILD-TYPE 77 46  4  3
D84V12, multiclass
    clus
vv   KIAA0586 MUTATED KIAA0586 WILD-TYPE
  R0                2                 77
  R1                4                 46
  R2                0                  4
  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"
D84V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA0586 MUTATED       0                         0     5
  KIAA0586 WILD-TYPE     9                         5   123
D84V14, multiclass
                           clus
vv                          KIAA0586 MUTATED KIAA0586 WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                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"
D84V15, binary
                    cls
clus                   0   1
  KIAA0586 MUTATED     0   5
  KIAA0586 WILD-TYPE   5 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0586 MUTATED      0    5
  KIAA0586 WILD-TYPE    5  100
                        clus
vv                       KIAA0586 MUTATED KIAA0586 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                5                100
[1] 2 2
[1] FALSE

Clustering(85) Variable = SYT14 MUTATION ANALYSIS
D85V1, survival
                 sevent
clus2              0  1
  SYT14 MUTATED    0  4
  SYT14 WILD-TYPE 68 72
  SYT14 MUTATED SYT14 WILD-TYPE 
              4             140 
  SYT14 MUTATED SYT14 WILD-TYPE 
              4              72 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  SYT14 MUTATED SYT14 WILD-TYPE 
           3.62            0.03 
  SYT14 MUTATED SYT14 WILD-TYPE 
          19.82           75.12 
  SYT14 MUTATED SYT14 WILD-TYPE 
          7.465          14.435 
[1] "3.6 - 19.8 (7.5)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "3.8"
D85V2, 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        3        8        23        99         4        4
D85V3, multiclass
           clus
vv          SYT14 MUTATED SYT14 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   121
D85V4, multiclass
       clus
vv      SYT14 MUTATED SYT14 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D85V5, binary
                 cls
clus                0   1
  SYT14 MUTATED     0   4
  SYT14 WILD-TYPE  37 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      0    4
  SYT14 WILD-TYPE   37  104
   clus
vv  SYT14 MUTATED SYT14 WILD-TYPE
  0             0              37
  1             4             104
[1] 2 2
[1] FALSE
D85V6, binary
                 cls
clus               0  1
  SYT14 MUTATED    3  0
  SYT14 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      3    0
  SYT14 WILD-TYPE   63    4
   clus
vv  SYT14 MUTATED SYT14 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D85V7, binary
                 cls
clus               0  1
  SYT14 MUTATED    2  2
  SYT14 WILD-TYPE 65 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      2    2
  SYT14 WILD-TYPE   65   77
        clus
vv       SYT14 MUTATED SYT14 WILD-TYPE
  FEMALE             2              65
  MALE               2              77
[1] 2 2
[1] FALSE
D85V8, binary
                 cls
clus               0  1
  SYT14 MUTATED    4  0
  SYT14 WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      4    0
  SYT14 WILD-TYPE   90   36
     clus
vv    SYT14 MUTATED SYT14 WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYT14 MUTATED                                     3
  SYT14 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYT14 MUTATED                                       1
  SYT14 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYT14 MUTATED                                                  0
  SYT14 WILD-TYPE                                                2
D85V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D85V10, continuous
[1] "Remove cluster labels:" "SYT14 MUTATED"         
clus
  SYT14 MUTATED SYT14 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-IB-AAUU      TCGA-LB-A7SX 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
D85V11, continuous
[1] "Remove cluster labels:" "SYT14 MUTATED"         
clus
  SYT14 MUTATED SYT14 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"SYT14 WILD-TYPE" "SYT14 WILD-TYPE" "SYT14 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SYT14 MUTATED    2  2  0  0
  SYT14 WILD-TYPE 77 48  4  3
D85V12, multiclass
    clus
vv   SYT14 MUTATED SYT14 WILD-TYPE
  R0             2              77
  R1             2              48
  R2             0               4
  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"
D85V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYT14 MUTATED       0                         0     4
  SYT14 WILD-TYPE     9                         5   124
D85V14, multiclass
                           clus
vv                          SYT14 MUTATED SYT14 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V15, binary
                 cls
clus                0   1
  SYT14 MUTATED     0   3
  SYT14 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      0    3
  SYT14 WILD-TYPE    5  102
                        clus
vv                       SYT14 MUTATED SYT14 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(86) Variable = TAX1BP1 MUTATION ANALYSIS
D86V1, survival
                   sevent
clus2                0  1
  TAX1BP1 MUTATED    1  4
  TAX1BP1 WILD-TYPE 67 72
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                5               139 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                4                72 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       20.19        23.21        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
            12.00              0.03 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
            41.33             75.12 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
            17.03             14.17 
[1] "12.0 - 41.3 (17.0)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "1.3"
D86V2, 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        3        8        23        98         4        4
D86V3, multiclass
           clus
vv          TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               0                23
  STAGE IIB               5                98
  STAGE III               0                 4
  STAGE IV                0                 4
[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   4  16   120
D86V4, multiclass
       clus
vv      TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  T1                  0                 4
  T2                  0                16
  T3+T4               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"
D86V5, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED     0   5
  TAX1BP1 WILD-TYPE  37 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      0    5
  TAX1BP1 WILD-TYPE   37  103
   clus
vv  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  0               0                37
  1               5               103
[1] 2 2
[1] FALSE
D86V6, binary
                   cls
clus                 0  1
  TAX1BP1 MUTATED    3  0
  TAX1BP1 WILD-TYPE 63  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      3    0
  TAX1BP1 WILD-TYPE   63    4
   clus
vv  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  0               3                63
  1               0                 4
[1] 2 2
[1] FALSE
D86V7, binary
                   cls
clus                 0  1
  TAX1BP1 MUTATED    2  3
  TAX1BP1 WILD-TYPE 65 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      2    3
  TAX1BP1 WILD-TYPE   65   76
        clus
vv       TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  FEMALE               2                65
  MALE                 3                76
[1] 2 2
[1] FALSE
D86V8, binary
                   cls
clus                 0  1
  TAX1BP1 MUTATED    4  0
  TAX1BP1 WILD-TYPE 90 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      4    0
  TAX1BP1 WILD-TYPE   90   36
     clus
vv    TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  NO                4                90
  YES               0                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TAX1BP1 MUTATED                                     5
  TAX1BP1 WILD-TYPE                                 125
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TAX1BP1 MUTATED                                       0
  TAX1BP1 WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TAX1BP1 MUTATED                                                  0
  TAX1BP1 WILD-TYPE                                                2
D86V9, 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                            125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D86V10, continuous
[1] "Remove cluster labels:" "TAX1BP1 MUTATED"       
clus
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                2                48 
       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-HV-AA8V        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-7887 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
D86V11, continuous
[1] "Remove cluster labels:" "TAX1BP1 MUTATED"       
clus
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                2                38 
       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-XN-A8T5        TCGA-YY-A8LH 
"TAX1BP1 WILD-TYPE" "TAX1BP1 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  TAX1BP1 MUTATED    4  0  0  1
  TAX1BP1 WILD-TYPE 75 50  4  2
D86V12, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  R0               4                75
  R1               0                50
  R2               0                 4
  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"
D86V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAX1BP1 MUTATED       0                         1     4
  TAX1BP1 WILD-TYPE     9                         4   124
D86V14, multiclass
                           clus
vv                          TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               1                 4
  WHITE                                   4               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V15, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED     0   4
  TAX1BP1 WILD-TYPE   5 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      0    4
  TAX1BP1 WILD-TYPE    5  101
                        clus
vv                       TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4               101
[1] 2 2
[1] FALSE

Clustering(87) Variable = HSPE1 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2              0  1
  HSPE1 MUTATED    2  2
  HSPE1 WILD-TYPE 66 74
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              4             140 
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              2              74 
$`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        42.31        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        58.98        43.50        20.84        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
        5.26         1.08         0.23        19.82        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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  HSPE1 MUTATED HSPE1 WILD-TYPE 
           6.38            0.03 
  HSPE1 MUTATED HSPE1 WILD-TYPE 
          24.26           75.12 
  HSPE1 MUTATED HSPE1 WILD-TYPE 
          9.105          14.435 
[1] "6.4 - 24.3 (9.1)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "1.2"
D87V2, 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        3        8        23        99         4        4
D87V3, multiclass
           clus
vv          HSPE1 MUTATED HSPE1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   121
D87V4, multiclass
       clus
vv      HSPE1 MUTATED HSPE1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D87V5, binary
                 cls
clus                0   1
  HSPE1 MUTATED     0   4
  HSPE1 WILD-TYPE  37 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPE1 MUTATED      0    4
  HSPE1 WILD-TYPE   37  104
   clus
vv  HSPE1 MUTATED HSPE1 WILD-TYPE
  0             0              37
  1             4             104
[1] 2 2
[1] FALSE
D87V6, binary
                 cls
clus               0  1
  HSPE1 MUTATED    0  0
  HSPE1 WILD-TYPE 66  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPE1 MUTATED      0    0
  HSPE1 WILD-TYPE   66    4
D87V7, binary
                 cls
clus               0  1
  HSPE1 MUTATED    2  2
  HSPE1 WILD-TYPE 65 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPE1 MUTATED      2    2
  HSPE1 WILD-TYPE   65   77
        clus
vv       HSPE1 MUTATED HSPE1 WILD-TYPE
  FEMALE             2              65
  MALE               2              77
[1] 2 2
[1] FALSE
D87V8, binary
                 cls
clus               0  1
  HSPE1 MUTATED    2  1
  HSPE1 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPE1 MUTATED      2    1
  HSPE1 WILD-TYPE   92   35
     clus
vv    HSPE1 MUTATED HSPE1 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HSPE1 MUTATED                                     3
  HSPE1 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HSPE1 MUTATED                                       1
  HSPE1 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HSPE1 MUTATED                                                  0
  HSPE1 WILD-TYPE                                                2
D87V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D87V10, continuous
[1] "Remove cluster labels:" "HSPE1 MUTATED"         
clus
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              1              49 
     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-HV-AA8V 
"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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
     TCGA-YY-A8LH 
"HSPE1 WILD-TYPE" 
D87V11, continuous
[1] "Remove cluster labels:" "HSPE1 MUTATED"         
clus
  HSPE1 MUTATED HSPE1 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" "HSPE1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  HSPE1 MUTATED    3  1  0  0
  HSPE1 WILD-TYPE 76 49  4  3
D87V12, multiclass
    clus
vv   HSPE1 MUTATED HSPE1 WILD-TYPE
  R0             3              76
  R1             1              49
  R2             0               4
  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"
D87V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HSPE1 MUTATED       0                         0     4
  HSPE1 WILD-TYPE     9                         5   124
D87V14, multiclass
                           clus
vv                          HSPE1 MUTATED HSPE1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V15, binary
                 cls
clus                0   1
  HSPE1 MUTATED     0   3
  HSPE1 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPE1 MUTATED      0    3
  HSPE1 WILD-TYPE    5  102
                        clus
vv                       HSPE1 MUTATED HSPE1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(88) Variable = GPSM2 MUTATION ANALYSIS
D88V1, survival
                 sevent
clus2              0  1
  GPSM2 MUTATED    1  2
  GPSM2 WILD-TYPE 67 74
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3             141 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              2              74 
$`GPSM2 MUTATED`
TCGA-F2-A44G TCGA-FB-A545 TCGA-IB-7886 
        7.66        12.66         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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  GPSM2 MUTATED GPSM2 WILD-TYPE 
           4.04            0.03 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
          12.66           75.12 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
           7.66           14.47 
[1] "4.0 - 12.7 (7.7)"  "0.0 - 75.1 (14.5)"
[1] "hr=" "3.5"
D88V2, 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        3        8        23       100         4        4
D88V3, multiclass
           clus
vv          GPSM2 MUTATED GPSM2 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D88V4, multiclass
       clus
vv      GPSM2 MUTATED GPSM2 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D88V5, binary
                 cls
clus                0   1
  GPSM2 MUTATED     0   3
  GPSM2 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      0    3
  GPSM2 WILD-TYPE   37  105
   clus
vv  GPSM2 MUTATED GPSM2 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D88V6, binary
                 cls
clus               0  1
  GPSM2 MUTATED    3  0
  GPSM2 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      3    0
  GPSM2 WILD-TYPE   63    4
   clus
vv  GPSM2 MUTATED GPSM2 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D88V7, binary
                 cls
clus               0  1
  GPSM2 MUTATED    2  1
  GPSM2 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      2    1
  GPSM2 WILD-TYPE   65   78
        clus
vv       GPSM2 MUTATED GPSM2 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D88V8, binary
                 cls
clus               0  1
  GPSM2 MUTATED    1  2
  GPSM2 WILD-TYPE 93 34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      1    2
  GPSM2 WILD-TYPE   93   34
     clus
vv    GPSM2 MUTATED GPSM2 WILD-TYPE
  NO              1              93
  YES             2              34
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPSM2 MUTATED                                     3
  GPSM2 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPSM2 MUTATED                                       0
  GPSM2 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPSM2 MUTATED                                                  0
  GPSM2 WILD-TYPE                                                2
D88V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D88V10, continuous
[1] "Remove cluster labels:" "GPSM2 MUTATED"         
clus
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-YY-A8LH 
"GPSM2 WILD-TYPE" 
D88V11, continuous
[1] "Remove cluster labels:" "GPSM2 MUTATED"         
clus
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  GPSM2 MUTATED    0  2  0  0
  GPSM2 WILD-TYPE 79 48  4  3
D88V12, multiclass
[1] "Remove cluster labels:" "GPSM2 MUTATED"         
clus
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              2             134 
     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-HV-A5A6      TCGA-HV-A7OL      TCGA-HV-AA8V 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-HV-AA8X      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-HZ-A9TJ      TCGA-IB-7644      TCGA-IB-7645      TCGA-IB-7646 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7647      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7652 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-7887      TCGA-IB-7888      TCGA-IB-7889 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-7890      TCGA-IB-7891      TCGA-IB-7893      TCGA-IB-7897 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SO      TCGA-IB-A5SP 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-A5SQ      TCGA-IB-A5SS      TCGA-IB-A5ST      TCGA-IB-A6UF 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP      TCGA-IB-AAUQ 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A8F3      TCGA-LB-A9Q5      TCGA-M8-A5N4 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-RB-AA9M      TCGA-S4-A8RM      TCGA-S4-A8RO      TCGA-S4-A8RP 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-US-A774      TCGA-US-A776      TCGA-US-A779      TCGA-US-A77E 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-US-A77G      TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
     TCGA-YY-A8LH      TCGA-Z5-AAPL 
"GPSM2 WILD-TYPE" "GPSM2 WILD-TYPE" 
D88V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPSM2 MUTATED       0                         0     3
  GPSM2 WILD-TYPE     9                         5   125
D88V14, multiclass
                           clus
vv                          GPSM2 MUTATED GPSM2 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V15, binary
                 cls
clus                0   1
  GPSM2 MUTATED     0   3
  GPSM2 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      0    3
  GPSM2 WILD-TYPE    5  102
                        clus
vv                       GPSM2 MUTATED GPSM2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(89) Variable = HELZ MUTATION ANALYSIS
D89V1, survival
                sevent
clus2             0  1
  HELZ MUTATED    0  5
  HELZ WILD-TYPE 68 71
  HELZ MUTATED HELZ WILD-TYPE 
             5            139 
  HELZ MUTATED HELZ WILD-TYPE 
             5             71 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  HELZ MUTATED HELZ WILD-TYPE 
         12.53           0.03 
  HELZ MUTATED HELZ WILD-TYPE 
         20.19          75.12 
  HELZ MUTATED HELZ WILD-TYPE 
         15.35          14.17 
[1] "12.5 - 20.2 (15.3)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "2"  
D89V2, 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        3        8        22       100         4        3
D89V3, multiclass
           clus
vv          HELZ MUTATED HELZ WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            1             22
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             1              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
  HELZ MUTATED     0   0     5
  HELZ WILD-TYPE   4  16   120
D89V4, multiclass
       clus
vv      HELZ MUTATED HELZ WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D89V5, binary
                cls
clus               0   1
  HELZ MUTATED     1   4
  HELZ WILD-TYPE  36 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELZ MUTATED      1    4
  HELZ WILD-TYPE   36  104
   clus
vv  HELZ MUTATED HELZ WILD-TYPE
  0            1             36
  1            4            104
[1] 2 2
[1] FALSE
D89V6, binary
                cls
clus              0  1
  HELZ MUTATED    2  1
  HELZ WILD-TYPE 64  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELZ MUTATED      2    1
  HELZ WILD-TYPE   64    3
   clus
vv  HELZ MUTATED HELZ WILD-TYPE
  0            2             64
  1            1              3
[1] 2 2
[1] FALSE
D89V7, binary
                cls
clus              0  1
  HELZ MUTATED    4  1
  HELZ WILD-TYPE 63 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELZ MUTATED      4    1
  HELZ WILD-TYPE   63   78
        clus
vv       HELZ MUTATED HELZ WILD-TYPE
  FEMALE            4             63
  MALE              1             78
[1] 2 2
[1] FALSE
D89V8, binary
                cls
clus              0  1
  HELZ MUTATED    5  0
  HELZ WILD-TYPE 89 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELZ MUTATED      5    0
  HELZ WILD-TYPE   89   36
     clus
vv    HELZ MUTATED HELZ WILD-TYPE
  NO             5             89
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HELZ MUTATED                                     5
  HELZ WILD-TYPE                                 125
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HELZ MUTATED                                       0
  HELZ WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HELZ MUTATED                                                  0
  HELZ WILD-TYPE                                                2
D89V9, multiclass
                                                  clus
vv                                                 HELZ MUTATED HELZ WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D89V10, continuous
D89V11, continuous
                vv
clus             R0 R1 R2 RX
  HELZ MUTATED    2  3  0  0
  HELZ WILD-TYPE 77 47  4  3
D89V12, multiclass
    clus
vv   HELZ MUTATED HELZ WILD-TYPE
  R0            2             77
  R1            3             47
  R2            0              4
  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"
D89V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HELZ MUTATED       1                         0     3
  HELZ WILD-TYPE     8                         5   125
D89V14, multiclass
                           clus
vv                          HELZ MUTATED HELZ WILD-TYPE
  ASIAN                                1              8
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V15, binary
                cls
clus               0   1
  HELZ MUTATED     0   4
  HELZ WILD-TYPE   5 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELZ MUTATED      0    4
  HELZ WILD-TYPE    5  101
                        clus
vv                       HELZ MUTATED HELZ WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(90) Variable = DOCK8 MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2              0  1
  DOCK8 MUTATED    3  2
  DOCK8 WILD-TYPE 65 74
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              5             139 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              2              74 
$`DOCK8 MUTATED`
TCGA-2J-AAB4 TCGA-3A-A9IB TCGA-HV-A5A5 TCGA-IB-7651 TCGA-IB-8127 
       23.97         7.36         9.50        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        42.31        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 
       58.98        43.50        20.84        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
       13.84         4.21         7.63        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  DOCK8 MUTATED DOCK8 WILD-TYPE 
           7.36            0.03 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
          23.97           75.12 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
          17.16           14.17 
[1] "7.4 - 24.0 (17.2)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.4"
D90V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DOCK8 MUTATED          0        0         0         5         0        0
  DOCK8 WILD-TYPE        3        8        23        98         4        4
D90V3, multiclass
           clus
vv          DOCK8 MUTATED DOCK8 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              0               4
[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     4
  DOCK8 WILD-TYPE   4  15   121
D90V4, multiclass
       clus
vv      DOCK8 MUTATED DOCK8 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D90V5, binary
                 cls
clus                0   1
  DOCK8 MUTATED     0   5
  DOCK8 WILD-TYPE  37 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED      0    5
  DOCK8 WILD-TYPE   37  103
   clus
vv  DOCK8 MUTATED DOCK8 WILD-TYPE
  0             0              37
  1             5             103
[1] 2 2
[1] FALSE
D90V6, binary
                 cls
clus               0  1
  DOCK8 MUTATED    4  0
  DOCK8 WILD-TYPE 62  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED      4    0
  DOCK8 WILD-TYPE   62    4
   clus
vv  DOCK8 MUTATED DOCK8 WILD-TYPE
  0             4              62
  1             0               4
[1] 2 2
[1] FALSE
D90V7, binary
                 cls
clus               0  1
  DOCK8 MUTATED    3  2
  DOCK8 WILD-TYPE 64 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED      3    2
  DOCK8 WILD-TYPE   64   77
        clus
vv       DOCK8 MUTATED DOCK8 WILD-TYPE
  FEMALE             3              64
  MALE               2              77
[1] 2 2
[1] FALSE
D90V8, binary
                 cls
clus               0  1
  DOCK8 MUTATED    5  0
  DOCK8 WILD-TYPE 89 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED      5    0
  DOCK8 WILD-TYPE   89   36
     clus
vv    DOCK8 MUTATED DOCK8 WILD-TYPE
  NO              5              89
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DOCK8 MUTATED                                     4
  DOCK8 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DOCK8 MUTATED                                       1
  DOCK8 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DOCK8 MUTATED                                                  0
  DOCK8 WILD-TYPE                                                2
D90V9, multiclass
                                                  clus
vv                                                 DOCK8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 DOCK8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D90V10, continuous
D90V11, continuous
                 vv
clus              R0 R1 R2 RX
  DOCK8 MUTATED    3  1  0  0
  DOCK8 WILD-TYPE 76 49  4  3
D90V12, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  R0             3              76
  R1             1              49
  R2             0               4
  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"
D90V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DOCK8 MUTATED       1                         0     4
  DOCK8 WILD-TYPE     8                         5   124
D90V14, multiclass
                           clus
vv                          DOCK8 MUTATED DOCK8 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V15, binary
                 cls
clus                0   1
  DOCK8 MUTATED     0   3
  DOCK8 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED      0    3
  DOCK8 WILD-TYPE    5  102
                        clus
vv                       DOCK8 MUTATED DOCK8 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(91) Variable = COBL MUTATION ANALYSIS
D91V1, survival
                sevent
clus2             0  1
  COBL MUTATED    3  3
  COBL WILD-TYPE 65 73
  COBL MUTATED COBL WILD-TYPE 
             6            138 
  COBL MUTATED COBL WILD-TYPE 
             3             73 
$`COBL MUTATED`
TCGA-FB-A545 TCGA-HZ-7925 TCGA-HZ-8519 TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-AAUS 
       12.66        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-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-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 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  COBL MUTATED COBL WILD-TYPE 
          4.04           0.03 
  COBL MUTATED COBL WILD-TYPE 
         20.19          75.12 
  COBL MUTATED COBL WILD-TYPE 
        13.795         14.285 
[1] "4.0 - 20.2 (13.8)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.2"
D91V2, 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        2        8        23        98         4        4
D91V3, multiclass
           clus
vv          COBL MUTATED COBL WILD-TYPE
  STAGE IA             1              2
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            5             98
  STAGE III            0              4
  STAGE IV             0              4
[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   3  16   120
D91V4, multiclass
       clus
vv      COBL MUTATED COBL WILD-TYPE
  T1               1              3
  T2               0             16
  T3+T4            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"
D91V5, binary
                cls
clus               0   1
  COBL MUTATED     1   5
  COBL WILD-TYPE  36 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  COBL MUTATED      1    5
  COBL WILD-TYPE   36  103
   clus
vv  COBL MUTATED COBL WILD-TYPE
  0            1             36
  1            5            103
[1] 2 2
[1] FALSE
D91V6, binary
                cls
clus              0  1
  COBL MUTATED    4  0
  COBL WILD-TYPE 62  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  COBL MUTATED      4    0
  COBL WILD-TYPE   62    4
   clus
vv  COBL MUTATED COBL WILD-TYPE
  0            4             62
  1            0              4
[1] 2 2
[1] FALSE
D91V7, binary
                cls
clus              0  1
  COBL MUTATED    3  3
  COBL WILD-TYPE 64 76
[1] "tbl2"
                cls
clus             [,1] [,2]
  COBL MUTATED      3    3
  COBL WILD-TYPE   64   76
        clus
vv       COBL MUTATED COBL WILD-TYPE
  FEMALE            3             64
  MALE              3             76
[1] 2 2
[1] FALSE
D91V8, binary
                cls
clus              0  1
  COBL MUTATED    4  2
  COBL WILD-TYPE 90 34
[1] "tbl2"
                cls
clus             [,1] [,2]
  COBL MUTATED      4    2
  COBL WILD-TYPE   90   34
     clus
vv    COBL MUTATED COBL WILD-TYPE
  NO             4             90
  YES            2             34
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  COBL MUTATED                                     5
  COBL WILD-TYPE                                 125
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  COBL MUTATED                                       1
  COBL WILD-TYPE                                    12
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  COBL MUTATED                                                  0
  COBL WILD-TYPE                                                2
D91V9, multiclass
                                                  clus
vv                                                 COBL MUTATED COBL WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5            125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             12
  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"
D91V10, continuous
D91V11, continuous
                vv
clus             R0 R1 R2 RX
  COBL MUTATED    3  2  0  0
  COBL WILD-TYPE 76 48  4  3
D91V12, multiclass
    clus
vv   COBL MUTATED COBL WILD-TYPE
  R0            3             76
  R1            2             48
  R2            0              4
  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"
D91V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  COBL MUTATED       0                         0     6
  COBL WILD-TYPE     9                         5   122
D91V14, multiclass
                           clus
vv                          COBL MUTATED COBL WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                6            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"
D91V15, binary
                cls
clus              0  1
  COBL MUTATED    0  6
  COBL WILD-TYPE  5 99
[1] "tbl2"
                cls
clus             [,1] [,2]
  COBL MUTATED      0    6
  COBL WILD-TYPE    5   99
                        clus
vv                       COBL MUTATED COBL WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            6             99
[1] 2 2
[1] FALSE

Clustering(92) Variable = GSN MUTATION ANALYSIS
D92V1, survival
               sevent
clus2            0  1
  GSN MUTATED    3  1
  GSN WILD-TYPE 65 75
  GSN MUTATED GSN WILD-TYPE 
            4           140 
  GSN MUTATED GSN WILD-TYPE 
            1            75 
$`GSN MUTATED`
TCGA-FB-A545 TCGA-HZ-A49H TCGA-IB-7651 TCGA-M8-A5N4 
       12.66        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  GSN MUTATED GSN WILD-TYPE 
        12.66          0.03 
  GSN MUTATED GSN WILD-TYPE 
        19.82         75.12 
  GSN MUTATED GSN WILD-TYPE 
       17.670        14.155 
[1] "12.7 - 19.8 (17.7)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "2.3"
D92V2, 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        3        8        22       100         4        4
D92V3, multiclass
           clus
vv          GSN MUTATED GSN WILD-TYPE
  STAGE IA            0             3
  STAGE IB            0             8
  STAGE IIA           1            22
  STAGE IIB           3           100
  STAGE III           0             4
  STAGE IV            0             4
[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   4  16   121
D92V4, multiclass
       clus
vv      GSN MUTATED GSN WILD-TYPE
  T1              0             4
  T2              0            16
  T3+T4           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"
D92V5, binary
               cls
clus              0   1
  GSN MUTATED     1   3
  GSN WILD-TYPE  36 105
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSN MUTATED      1    3
  GSN WILD-TYPE   36  105
   clus
vv  GSN MUTATED GSN WILD-TYPE
  0           1            36
  1           3           105
[1] 2 2
[1] FALSE
D92V6, binary
               cls
clus             0  1
  GSN MUTATED    3  0
  GSN WILD-TYPE 63  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSN MUTATED      3    0
  GSN WILD-TYPE   63    4
   clus
vv  GSN MUTATED GSN WILD-TYPE
  0           3            63
  1           0             4
[1] 2 2
[1] FALSE
D92V7, binary
               cls
clus             0  1
  GSN MUTATED    4  0
  GSN WILD-TYPE 63 79
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSN MUTATED      4    0
  GSN WILD-TYPE   63   79
        clus
vv       GSN MUTATED GSN WILD-TYPE
  FEMALE           4            63
  MALE             0            79
[1] 2 2
[1] FALSE
D92V8, binary
               cls
clus             0  1
  GSN MUTATED    2  2
  GSN WILD-TYPE 92 34
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSN MUTATED      2    2
  GSN WILD-TYPE   92   34
     clus
vv    GSN MUTATED GSN WILD-TYPE
  NO            2            92
  YES           2            34
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GSN MUTATED                                     4
  GSN WILD-TYPE                                 126
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GSN MUTATED                                       0
  GSN WILD-TYPE                                    13
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GSN MUTATED                                                  0
  GSN WILD-TYPE                                                2
D92V9, multiclass
                                                  clus
vv                                                 GSN MUTATED GSN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            13
  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"
D92V10, continuous
[1] "Remove cluster labels:" "GSN MUTATED"           
clus
  GSN MUTATED GSN WILD-TYPE 
            1            49 
   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-HV-AA8V    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-HZ-A8P1    TCGA-IB-7644 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-IB-7649    TCGA-IB-7885    TCGA-IB-7886    TCGA-IB-7887    TCGA-IB-7891 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-8127    TCGA-IB-A5SS    TCGA-IB-A6UF    TCGA-IB-A6UG 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-IB-A7M4    TCGA-IB-AAUQ    TCGA-IB-AAUS    TCGA-IB-AAUT    TCGA-IB-AAUU 
"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-S4-A8RP 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
   TCGA-US-A774    TCGA-XD-AAUL    TCGA-XN-A8T5    TCGA-YY-A8LH 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
D92V11, continuous
[1] "Remove cluster labels:" "GSN MUTATED"           
clus
  GSN MUTATED GSN WILD-TYPE 
            1            39 
   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-XN-A8T5    TCGA-YY-A8LH 
"GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" "GSN WILD-TYPE" 
               vv
clus            R0 R1 R2 RX
  GSN MUTATED    2  1  0  0
  GSN WILD-TYPE 77 49  4  3
D92V12, multiclass
    clus
vv   GSN MUTATED GSN WILD-TYPE
  R0           2            77
  R1           1            49
  R2           0             4
  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"
D92V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GSN MUTATED       0                         0     3
  GSN WILD-TYPE     9                         5   125
D92V14, multiclass
                           clus
vv                          GSN MUTATED GSN WILD-TYPE
  ASIAN                               0             9
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               3           125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V15, binary
               cls
clus              0   1
  GSN MUTATED     0   3
  GSN WILD-TYPE   5 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSN MUTATED      0    3
  GSN WILD-TYPE    5  102
                        clus
vv                       GSN MUTATED GSN WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           3           102
[1] 2 2
[1] FALSE

Clustering(93) Variable = NAA20 MUTATION ANALYSIS
D93V1, survival
                 sevent
clus2              0  1
  NAA20 MUTATED    1  2
  NAA20 WILD-TYPE 67 74
  NAA20 MUTATED NAA20 WILD-TYPE 
              3             141 
  NAA20 MUTATED NAA20 WILD-TYPE 
              2              74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7651 
       19.82        12.95        49.38         4.77        21.90        19.82 
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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  NAA20 MUTATED NAA20 WILD-TYPE 
          15.35            0.03 
  NAA20 MUTATED NAA20 WILD-TYPE 
          41.33           75.12 
  NAA20 MUTATED NAA20 WILD-TYPE 
          20.19           14.14 
[1] "15.3 - 41.3 (20.2)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "1.2"
D93V2, 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        3        8        23       100         4        4
D93V3, multiclass
           clus
vv          NAA20 MUTATED NAA20 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D93V4, multiclass
       clus
vv      NAA20 MUTATED NAA20 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D93V5, binary
                 cls
clus                0   1
  NAA20 MUTATED     0   3
  NAA20 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA20 MUTATED      0    3
  NAA20 WILD-TYPE   37  105
   clus
vv  NAA20 MUTATED NAA20 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D93V6, binary
                 cls
clus               0  1
  NAA20 MUTATED    2  0
  NAA20 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA20 MUTATED      2    0
  NAA20 WILD-TYPE   64    4
   clus
vv  NAA20 MUTATED NAA20 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D93V7, binary
                 cls
clus               0  1
  NAA20 MUTATED    2  1
  NAA20 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA20 MUTATED      2    1
  NAA20 WILD-TYPE   65   78
        clus
vv       NAA20 MUTATED NAA20 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D93V8, binary
                 cls
clus               0  1
  NAA20 MUTATED    3  0
  NAA20 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA20 MUTATED      3    0
  NAA20 WILD-TYPE   91   36
     clus
vv    NAA20 MUTATED NAA20 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NAA20 MUTATED                                     3
  NAA20 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NAA20 MUTATED                                       0
  NAA20 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NAA20 MUTATED                                                  0
  NAA20 WILD-TYPE                                                2
D93V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D93V10, continuous
[1] "Remove cluster labels:" "NAA20 MUTATED"         
clus
  NAA20 MUTATED NAA20 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
D93V11, continuous
[1] "Remove cluster labels:" "NAA20 MUTATED"         
clus
  NAA20 MUTATED NAA20 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NAA20 MUTATED    2  1  0  0
  NAA20 WILD-TYPE 77 49  4  3
D93V12, multiclass
    clus
vv   NAA20 MUTATED NAA20 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D93V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAA20 MUTATED       0                         0     2
  NAA20 WILD-TYPE     9                         5   126
D93V14, multiclass
[1] "Remove cluster labels:" "NAA20 MUTATED"         
clus
  NAA20 MUTATED NAA20 WILD-TYPE 
              2             140 
     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-HV-A5A3 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HV-A5A4      TCGA-HV-A5A5      TCGA-HV-A5A6      TCGA-HV-A7OL 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7919      TCGA-HZ-7922 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-7926      TCGA-HZ-8001      TCGA-HZ-8002      TCGA-HZ-8003 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-8005      TCGA-HZ-8315      TCGA-HZ-8317      TCGA-HZ-8519 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-8636      TCGA-HZ-8637      TCGA-HZ-A49G      TCGA-HZ-A49H 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A4BH      TCGA-HZ-A4BK      TCGA-HZ-A77O 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-HZ-A9TJ      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-XN-A8T3      TCGA-XN-A8T5 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YH-A8SY      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" "NAA20 WILD-TYPE" 
D93V15, binary
                 cls
clus                0   1
  NAA20 MUTATED     0   2
  NAA20 WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA20 MUTATED      0    2
  NAA20 WILD-TYPE    5  103
                        clus
vv                       NAA20 MUTATED NAA20 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(94) Variable = ZACN MUTATION ANALYSIS
D94V1, survival
                sevent
clus2             0  1
  ZACN MUTATED    1  2
  ZACN WILD-TYPE 67 74
  ZACN MUTATED ZACN WILD-TYPE 
             3            141 
  ZACN MUTATED ZACN WILD-TYPE 
             2             74 
$`ZACN MUTATED`
TCGA-IB-A5SQ TCGA-US-A774 TCGA-US-A776 
        7.20        22.85        39.98 

$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-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-RB-AA9M TCGA-S4-A8RM 
       15.45        13.68         3.12        15.32         9.40        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       17.26        23.08        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  ZACN MUTATED ZACN WILD-TYPE 
          7.20           0.03 
  ZACN MUTATED ZACN WILD-TYPE 
         39.98          75.12 
  ZACN MUTATED ZACN WILD-TYPE 
         22.85          14.17 
[1] "7.2 - 40.0 (22.9)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.2"
D94V2, 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        3        7        22       102         4        4
D94V3, multiclass
           clus
vv          ZACN MUTATED ZACN WILD-TYPE
  STAGE IA             0              3
  STAGE IB             1              7
  STAGE IIA            1             22
  STAGE IIB            1            102
  STAGE III            0              4
  STAGE IV             0              4
[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   4  15   123
D94V4, multiclass
       clus
vv      ZACN MUTATED ZACN WILD-TYPE
  T1               0              4
  T2               1             15
  T3+T4            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"
D94V5, binary
                cls
clus               0   1
  ZACN MUTATED     2   1
  ZACN WILD-TYPE  35 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      2    1
  ZACN WILD-TYPE   35  107
   clus
vv  ZACN MUTATED ZACN WILD-TYPE
  0            2             35
  1            1            107
[1] 2 2
[1] FALSE
D94V6, binary
                cls
clus              0  1
  ZACN MUTATED    1  0
  ZACN WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      1    0
  ZACN WILD-TYPE   65    4
   clus
vv  ZACN MUTATED ZACN WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D94V7, binary
                cls
clus              0  1
  ZACN MUTATED    2  1
  ZACN WILD-TYPE 65 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      2    1
  ZACN WILD-TYPE   65   78
        clus
vv       ZACN MUTATED ZACN WILD-TYPE
  FEMALE            2             65
  MALE              1             78
[1] 2 2
[1] FALSE
D94V8, binary
                cls
clus              0  1
  ZACN MUTATED    3  0
  ZACN WILD-TYPE 91 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      3    0
  ZACN WILD-TYPE   91   36
     clus
vv    ZACN MUTATED ZACN WILD-TYPE
  NO             3             91
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZACN MUTATED                                     2
  ZACN WILD-TYPE                                 128
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZACN MUTATED                                       0
  ZACN WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZACN MUTATED                                                  1
  ZACN WILD-TYPE                                                1
D94V9, multiclass
                                                  clus
vv                                                 ZACN MUTATED ZACN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2            128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D94V10, continuous
[1] "Remove cluster labels:" "ZACN MUTATED"          
clus
  ZACN MUTATED ZACN WILD-TYPE 
             1             49 
    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-HV-AA8V     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-7887     TCGA-IB-7891     TCGA-IB-8126 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-S4-A8RP     TCGA-XD-AAUL     TCGA-XN-A8T5 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
    TCGA-YY-A8LH 
"ZACN WILD-TYPE" 
D94V11, continuous
[1] "Remove cluster labels:" "ZACN MUTATED"          
clus
  ZACN MUTATED ZACN WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"ZACN WILD-TYPE" "ZACN WILD-TYPE" "ZACN WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  ZACN MUTATED    3  0  0  0
  ZACN WILD-TYPE 76 50  4  3
D94V12, multiclass
    clus
vv   ZACN MUTATED ZACN WILD-TYPE
  R0            3             76
  R1            0             50
  R2            0              4
  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"
D94V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZACN MUTATED       0                         0     3
  ZACN WILD-TYPE     9                         5   125
D94V14, multiclass
                           clus
vv                          ZACN MUTATED ZACN WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V15, binary
                cls
clus               0   1
  ZACN MUTATED     0   3
  ZACN WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZACN MUTATED      0    3
  ZACN WILD-TYPE    5  102
                        clus
vv                       ZACN MUTATED ZACN WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(95) Variable = AP3B1 MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2              0  1
  AP3B1 MUTATED    2  2
  AP3B1 WILD-TYPE 66 74
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              4             140 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              2              74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       20.19        17.03        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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        24.23        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  AP3B1 MUTATED AP3B1 WILD-TYPE 
           3.62            0.03 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
          23.21           75.12 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
         18.540          14.155 
[1] "3.6 - 23.2 (18.5)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.2"
D95V2, 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        3        8        23       100         3        4
D95V3, multiclass
           clus
vv          AP3B1 MUTATED AP3B1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             1               3
  STAGE IV              0               4
[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   4  16   121
D95V4, multiclass
       clus
vv      AP3B1 MUTATED AP3B1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D95V5, binary
                 cls
clus                0   1
  AP3B1 MUTATED     1   3
  AP3B1 WILD-TYPE  36 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      1    3
  AP3B1 WILD-TYPE   36  105
   clus
vv  AP3B1 MUTATED AP3B1 WILD-TYPE
  0             1              36
  1             3             105
[1] 2 2
[1] FALSE
D95V6, binary
                 cls
clus               0  1
  AP3B1 MUTATED    2  0
  AP3B1 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      2    0
  AP3B1 WILD-TYPE   64    4
   clus
vv  AP3B1 MUTATED AP3B1 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D95V7, binary
                 cls
clus               0  1
  AP3B1 MUTATED    3  1
  AP3B1 WILD-TYPE 64 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      3    1
  AP3B1 WILD-TYPE   64   78
        clus
vv       AP3B1 MUTATED AP3B1 WILD-TYPE
  FEMALE             3              64
  MALE               1              78
[1] 2 2
[1] FALSE
D95V8, binary
                 cls
clus               0  1
  AP3B1 MUTATED    3  1
  AP3B1 WILD-TYPE 91 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      3    1
  AP3B1 WILD-TYPE   91   35
     clus
vv    AP3B1 MUTATED AP3B1 WILD-TYPE
  NO              3              91
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AP3B1 MUTATED                                     4
  AP3B1 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AP3B1 MUTATED                                       0
  AP3B1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AP3B1 MUTATED                                                  0
  AP3B1 WILD-TYPE                                                2
D95V9, 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                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D95V10, continuous
[1] "Remove cluster labels:" "AP3B1 MUTATED"         
clus
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-IB-AAUU      TCGA-LB-A7SX 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
D95V11, continuous
[1] "Remove cluster labels:" "AP3B1 MUTATED"         
clus
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" "AP3B1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  AP3B1 MUTATED    2  2  0  0
  AP3B1 WILD-TYPE 77 48  4  3
D95V12, multiclass
    clus
vv   AP3B1 MUTATED AP3B1 WILD-TYPE
  R0             2              77
  R1             2              48
  R2             0               4
  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"
D95V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AP3B1 MUTATED       0                         0     4
  AP3B1 WILD-TYPE     9                         5   124
D95V14, multiclass
                           clus
vv                          AP3B1 MUTATED AP3B1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V15, binary
                 cls
clus                0   1
  AP3B1 MUTATED     0   4
  AP3B1 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      0    4
  AP3B1 WILD-TYPE    5  101
                        clus
vv                       AP3B1 MUTATED AP3B1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(96) Variable = C3ORF15 MUTATION ANALYSIS
D96V1, survival
                   sevent
clus2                0  1
  C3ORF15 MUTATED    2  3
  C3ORF15 WILD-TYPE 66 73
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
                5               139 
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
                3                73 
$`C3ORF15 MUTATED`
TCGA-3A-A9I5 TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-AAUT TCGA-LB-A9Q5 
       58.98        12.95        19.82         9.44        10.29 

$`C3ORF15 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        42.31        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        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       19.82        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-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 
        6.02        11.11         7.40         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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
             9.44              0.03 
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
            58.98             75.12 
  C3ORF15 MUTATED C3ORF15 WILD-TYPE 
            12.95             14.40 
[1] "9.4 - 59.0 (12.9)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1"  
D96V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  C3ORF15 MUTATED          0        0         0         3         0        1
  C3ORF15 WILD-TYPE        3        8        23       100         4        3
D96V3, multiclass
           clus
vv          C3ORF15 MUTATED C3ORF15 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               0                23
  STAGE IIB               3               100
  STAGE III               0                 4
  STAGE IV                1                 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
  C3ORF15 MUTATED     0   1     3
  C3ORF15 WILD-TYPE   4  15   122
D96V4, multiclass
       clus
vv      C3ORF15 MUTATED C3ORF15 WILD-TYPE
  T1                  0                 4
  T2                  1                15
  T3+T4               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"
D96V5, binary
                   cls
clus                  0   1
  C3ORF15 MUTATED     1   4
  C3ORF15 WILD-TYPE  36 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      1    4
  C3ORF15 WILD-TYPE   36  104
   clus
vv  C3ORF15 MUTATED C3ORF15 WILD-TYPE
  0               1                36
  1               4               104
[1] 2 2
[1] FALSE
D96V6, binary
                   cls
clus                 0  1
  C3ORF15 MUTATED    2  1
  C3ORF15 WILD-TYPE 64  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      2    1
  C3ORF15 WILD-TYPE   64    3
   clus
vv  C3ORF15 MUTATED C3ORF15 WILD-TYPE
  0               2                64
  1               1                 3
[1] 2 2
[1] FALSE
D96V7, binary
                   cls
clus                 0  1
  C3ORF15 MUTATED    3  2
  C3ORF15 WILD-TYPE 64 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      3    2
  C3ORF15 WILD-TYPE   64   77
        clus
vv       C3ORF15 MUTATED C3ORF15 WILD-TYPE
  FEMALE               3                64
  MALE                 2                77
[1] 2 2
[1] FALSE
D96V8, binary
                   cls
clus                 0  1
  C3ORF15 MUTATED    3  2
  C3ORF15 WILD-TYPE 91 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      3    2
  C3ORF15 WILD-TYPE   91   34
     clus
vv    C3ORF15 MUTATED C3ORF15 WILD-TYPE
  NO                3                91
  YES               2                34
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C3ORF15 MUTATED                                     4
  C3ORF15 WILD-TYPE                                 126
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C3ORF15 MUTATED                                       0
  C3ORF15 WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C3ORF15 MUTATED                                                  1
  C3ORF15 WILD-TYPE                                                1
D96V9, multiclass
                                                  clus
vv                                                 C3ORF15 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 C3ORF15 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D96V10, continuous
D96V11, continuous
                   vv
clus                R0 R1 R2 RX
  C3ORF15 MUTATED    3  2  0  0
  C3ORF15 WILD-TYPE 76 48  4  3
D96V12, multiclass
    clus
vv   C3ORF15 MUTATED C3ORF15 WILD-TYPE
  R0               3                76
  R1               2                48
  R2               0                 4
  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"
D96V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C3ORF15 MUTATED       0                         0     5
  C3ORF15 WILD-TYPE     9                         5   123
D96V14, multiclass
                           clus
vv                          C3ORF15 MUTATED C3ORF15 WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               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"
D96V15, binary
                   cls
clus                  0   1
  C3ORF15 MUTATED     0   5
  C3ORF15 WILD-TYPE   5 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF15 MUTATED      0    5
  C3ORF15 WILD-TYPE    5  100
                        clus
vv                       C3ORF15 MUTATED C3ORF15 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5               100
[1] 2 2
[1] FALSE

Clustering(97) Variable = BCLAF1 MUTATION ANALYSIS
D97V1, survival
                  sevent
clus2               0  1
  BCLAF1 MUTATED    1  6
  BCLAF1 WILD-TYPE 67 70
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               7              137 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               6               70 
$`BCLAF1 MUTATED`
TCGA-2L-AAQE TCGA-3A-A9IB TCGA-HV-AA8X TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-A5SQ 
       22.49         7.36        17.49        12.95        19.82         7.20 
TCGA-M8-A5N4 
       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        42.31        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 
       58.98        43.50        20.84        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       30.25        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        19.59         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-HZ-A9TJ TCGA-IB-7645 
        5.26        10.85         1.08         0.23        19.82        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-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-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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
        0.39        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            7.20             0.03 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           22.49            75.12 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           17.49            14.17 
[1] "7.2 - 22.5 (17.5)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.8"
D97V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BCLAF1 MUTATED          0        1         1         4         0        1
  BCLAF1 WILD-TYPE        3        7        22        99         4        3
D97V3, multiclass
           clus
vv          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               1                7
  STAGE IIA              1               22
  STAGE IIB              4               99
  STAGE III              0                4
  STAGE IV               1                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
  BCLAF1 MUTATED     0   2     5
  BCLAF1 WILD-TYPE   4  14   120
D97V4, multiclass
       clus
vv      BCLAF1 MUTATED BCLAF1 WILD-TYPE
  T1                 0                4
  T2                 2               14
  T3+T4              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"
D97V5, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     2   5
  BCLAF1 WILD-TYPE  35 103
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      2    5
  BCLAF1 WILD-TYPE   35  103
   clus
vv  BCLAF1 MUTATED BCLAF1 WILD-TYPE
  0              2               35
  1              5              103
[1] 2 2
[1] FALSE
D97V6, binary
                  cls
clus                0  1
  BCLAF1 MUTATED    4  1
  BCLAF1 WILD-TYPE 62  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      4    1
  BCLAF1 WILD-TYPE   62    3
   clus
vv  BCLAF1 MUTATED BCLAF1 WILD-TYPE
  0              4               62
  1              1                3
[1] 2 2
[1] FALSE
D97V7, binary
                  cls
clus                0  1
  BCLAF1 MUTATED    6  1
  BCLAF1 WILD-TYPE 61 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      6    1
  BCLAF1 WILD-TYPE   61   78
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE              6               61
  MALE                1               78
[1] 2 2
[1] FALSE
D97V8, binary
                  cls
clus                0  1
  BCLAF1 MUTATED    6  1
  BCLAF1 WILD-TYPE 88 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      6    1
  BCLAF1 WILD-TYPE   88   35
     clus
vv    BCLAF1 MUTATED BCLAF1 WILD-TYPE
  NO               6               88
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BCLAF1 MUTATED                                     7
  BCLAF1 WILD-TYPE                                 123
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BCLAF1 MUTATED                                       0
  BCLAF1 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BCLAF1 MUTATED                                                  0
  BCLAF1 WILD-TYPE                                                2
D97V9, multiclass
                                                  clus
vv                                                 BCLAF1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 BCLAF1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D97V10, continuous
D97V11, continuous
                  vv
clus               R0 R1 R2 RX
  BCLAF1 MUTATED    4  2  1  0
  BCLAF1 WILD-TYPE 75 48  3  3
D97V12, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  R0              4               75
  R1              2               48
  R2              1                3
  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"
D97V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCLAF1 MUTATED       1                         0     5
  BCLAF1 WILD-TYPE     8                         5   123
D97V14, multiclass
                           clus
vv                          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  ASIAN                                  1                8
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              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"
D97V15, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     0   4
  BCLAF1 WILD-TYPE   5 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      0    4
  BCLAF1 WILD-TYPE    5  101
                        clus
vv                       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              101
[1] 2 2
[1] FALSE

Clustering(98) Variable = RBL2 MUTATION ANALYSIS
D98V1, survival
                sevent
clus2             0  1
  RBL2 MUTATED    2  2
  RBL2 WILD-TYPE 66 74
  RBL2 MUTATED RBL2 WILD-TYPE 
             4            140 
  RBL2 MUTATED RBL2 WILD-TYPE 
             2             74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       20.19        17.03        12.03        19.59         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-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       19.82        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-LB-A7SX TCGA-LB-A8F3 
        6.02        11.11         7.40         9.44        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  RBL2 MUTATED RBL2 WILD-TYPE 
          8.05           0.03 
  RBL2 MUTATED RBL2 WILD-TYPE 
         23.21          75.12 
  RBL2 MUTATED RBL2 WILD-TYPE 
        16.385         14.285 
[1] "8.1 - 23.2 (16.4)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.2"
D98V2, 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        3        8        23       101         3        3
D98V3, multiclass
           clus
vv          RBL2 MUTATED RBL2 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            2            101
  STAGE III            1              3
  STAGE IV             1              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
  RBL2 MUTATED     0   0     4
  RBL2 WILD-TYPE   4  16   121
D98V4, multiclass
       clus
vv      RBL2 MUTATED RBL2 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D98V5, binary
                cls
clus               0   1
  RBL2 MUTATED     1   3
  RBL2 WILD-TYPE  36 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      1    3
  RBL2 WILD-TYPE   36  105
   clus
vv  RBL2 MUTATED RBL2 WILD-TYPE
  0            1             36
  1            3            105
[1] 2 2
[1] FALSE
D98V6, binary
                cls
clus              0  1
  RBL2 MUTATED    2  1
  RBL2 WILD-TYPE 64  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      2    1
  RBL2 WILD-TYPE   64    3
   clus
vv  RBL2 MUTATED RBL2 WILD-TYPE
  0            2             64
  1            1              3
[1] 2 2
[1] FALSE
D98V7, binary
                cls
clus              0  1
  RBL2 MUTATED    2  2
  RBL2 WILD-TYPE 65 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      2    2
  RBL2 WILD-TYPE   65   77
        clus
vv       RBL2 MUTATED RBL2 WILD-TYPE
  FEMALE            2             65
  MALE              2             77
[1] 2 2
[1] FALSE
D98V8, binary
                cls
clus              0  1
  RBL2 MUTATED    4  0
  RBL2 WILD-TYPE 90 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      4    0
  RBL2 WILD-TYPE   90   36
     clus
vv    RBL2 MUTATED RBL2 WILD-TYPE
  NO             4             90
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBL2 MUTATED                                     4
  RBL2 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBL2 MUTATED                                       0
  RBL2 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBL2 MUTATED                                                  0
  RBL2 WILD-TYPE                                                2
D98V9, multiclass
                                                  clus
vv                                                 RBL2 MUTATED RBL2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D98V10, continuous
D98V11, continuous
[1] "Remove cluster labels:" "RBL2 MUTATED"          
clus
  RBL2 MUTATED RBL2 WILD-TYPE 
             2             38 
    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-XN-A8T5     TCGA-YY-A8LH 
"RBL2 WILD-TYPE" "RBL2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  RBL2 MUTATED    3  1  0  0
  RBL2 WILD-TYPE 76 49  4  3
D98V12, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  R0            3             76
  R1            1             49
  R2            0              4
  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"
D98V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBL2 MUTATED       0                         0     4
  RBL2 WILD-TYPE     9                         5   124
D98V14, multiclass
                           clus
vv                          RBL2 MUTATED RBL2 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V15, binary
                cls
clus               0   1
  RBL2 MUTATED     0   4
  RBL2 WILD-TYPE   5 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED      0    4
  RBL2 WILD-TYPE    5  101
                        clus
vv                       RBL2 MUTATED RBL2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(99) Variable = OMA1 MUTATION ANALYSIS
D99V1, survival
                sevent
clus2             0  1
  OMA1 MUTATED    0  3
  OMA1 WILD-TYPE 68 73
  OMA1 MUTATED OMA1 WILD-TYPE 
             3            141 
  OMA1 MUTATED OMA1 WILD-TYPE 
             3             73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
       20.19        17.03        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  OMA1 MUTATED OMA1 WILD-TYPE 
          3.62           0.03 
  OMA1 MUTATED OMA1 WILD-TYPE 
         19.82          75.12 
  OMA1 MUTATED OMA1 WILD-TYPE 
          3.95          14.40 
[1] "3.6 - 19.8 (4.0)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "3.7"
D99V2, 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        3        8        23       100         4        4
D99V3, multiclass
           clus
vv          OMA1 MUTATED OMA1 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   122
D99V4, multiclass
       clus
vv      OMA1 MUTATED OMA1 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D99V5, binary
                cls
clus               0   1
  OMA1 MUTATED     0   3
  OMA1 WILD-TYPE  37 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      0    3
  OMA1 WILD-TYPE   37  105
   clus
vv  OMA1 MUTATED OMA1 WILD-TYPE
  0            0             37
  1            3            105
[1] 2 2
[1] FALSE
D99V6, binary
                cls
clus              0  1
  OMA1 MUTATED    2  0
  OMA1 WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      2    0
  OMA1 WILD-TYPE   64    4
   clus
vv  OMA1 MUTATED OMA1 WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D99V7, binary
                cls
clus              0  1
  OMA1 MUTATED    2  1
  OMA1 WILD-TYPE 65 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      2    1
  OMA1 WILD-TYPE   65   78
        clus
vv       OMA1 MUTATED OMA1 WILD-TYPE
  FEMALE            2             65
  MALE              1             78
[1] 2 2
[1] FALSE
D99V8, binary
                cls
clus              0  1
  OMA1 MUTATED    3  0
  OMA1 WILD-TYPE 91 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      3    0
  OMA1 WILD-TYPE   91   36
     clus
vv    OMA1 MUTATED OMA1 WILD-TYPE
  NO             3             91
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OMA1 MUTATED                                     3
  OMA1 WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OMA1 MUTATED                                       0
  OMA1 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OMA1 MUTATED                                                  0
  OMA1 WILD-TYPE                                                2
D99V9, multiclass
                                                  clus
vv                                                 OMA1 MUTATED OMA1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D99V10, continuous
[1] "Remove cluster labels:" "OMA1 MUTATED"          
clus
  OMA1 MUTATED OMA1 WILD-TYPE 
             2             48 
    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-HV-AA8V     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-IB-AAUU     TCGA-LB-A7SX 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
D99V11, continuous
[1] "Remove cluster labels:" "OMA1 MUTATED"          
clus
  OMA1 MUTATED OMA1 WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"OMA1 WILD-TYPE" "OMA1 WILD-TYPE" "OMA1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  OMA1 MUTATED    1  2  0  0
  OMA1 WILD-TYPE 78 48  4  3
D99V12, multiclass
    clus
vv   OMA1 MUTATED OMA1 WILD-TYPE
  R0            1             78
  R1            2             48
  R2            0              4
  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"
D99V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OMA1 MUTATED       0                         0     3
  OMA1 WILD-TYPE     9                         5   125
D99V14, multiclass
                           clus
vv                          OMA1 MUTATED OMA1 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V15, binary
                cls
clus               0   1
  OMA1 MUTATED     0   3
  OMA1 WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  OMA1 MUTATED      0    3
  OMA1 WILD-TYPE    5  102
                        clus
vv                       OMA1 MUTATED OMA1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(100) Variable = SORT1 MUTATION ANALYSIS
D100V1, survival
                 sevent
clus2              0  1
  SORT1 MUTATED    3  2
  SORT1 WILD-TYPE 65 74
  SORT1 MUTATED SORT1 WILD-TYPE 
              5             139 
  SORT1 MUTATED SORT1 WILD-TYPE 
              2              74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-A9Q5 
       11.11         7.40         9.44         8.05        12.92        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SORT1 MUTATED SORT1 WILD-TYPE 
           3.62            0.03 
  SORT1 MUTATED SORT1 WILD-TYPE 
          23.21           75.12 
  SORT1 MUTATED SORT1 WILD-TYPE 
          19.27           14.17 
[1] "3.6 - 23.2 (19.3)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.4"
D100V2, 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        3        8        21       101         3        4
D100V3, multiclass
           clus
vv          SORT1 MUTATED SORT1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             2              21
  STAGE IIB             2             101
  STAGE III             1               3
  STAGE IV              0               4
[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   4  16   120
D100V4, multiclass
       clus
vv      SORT1 MUTATED SORT1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D100V5, binary
                 cls
clus                0   1
  SORT1 MUTATED     3   2
  SORT1 WILD-TYPE  34 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SORT1 MUTATED      3    2
  SORT1 WILD-TYPE   34  106
   clus
vv  SORT1 MUTATED SORT1 WILD-TYPE
  0             3              34
  1             2             106
[1] 2 2
[1] FALSE
D100V6, binary
                 cls
clus               0  1
  SORT1 MUTATED    3  0
  SORT1 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SORT1 MUTATED      3    0
  SORT1 WILD-TYPE   63    4
   clus
vv  SORT1 MUTATED SORT1 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D100V7, binary
                 cls
clus               0  1
  SORT1 MUTATED    3  2
  SORT1 WILD-TYPE 64 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SORT1 MUTATED      3    2
  SORT1 WILD-TYPE   64   77
        clus
vv       SORT1 MUTATED SORT1 WILD-TYPE
  FEMALE             3              64
  MALE               2              77
[1] 2 2
[1] FALSE
D100V8, binary
                 cls
clus               0  1
  SORT1 MUTATED    3  2
  SORT1 WILD-TYPE 91 34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SORT1 MUTATED      3    2
  SORT1 WILD-TYPE   91   34
     clus
vv    SORT1 MUTATED SORT1 WILD-TYPE
  NO              3              91
  YES             2              34
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SORT1 MUTATED                                     5
  SORT1 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SORT1 MUTATED                                       0
  SORT1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SORT1 MUTATED                                                  0
  SORT1 WILD-TYPE                                                2
D100V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D100V10, continuous
[1] "Remove cluster labels:" "SORT1 MUTATED"         
clus
  SORT1 MUTATED SORT1 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-IB-AAUU      TCGA-LB-A7SX 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
D100V11, continuous
[1] "Remove cluster labels:" "SORT1 MUTATED"         
clus
  SORT1 MUTATED SORT1 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"SORT1 WILD-TYPE" "SORT1 WILD-TYPE" "SORT1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SORT1 MUTATED    4  1  0  0
  SORT1 WILD-TYPE 75 49  4  3
D100V12, multiclass
    clus
vv   SORT1 MUTATED SORT1 WILD-TYPE
  R0             4              75
  R1             1              49
  R2             0               4
  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"
D100V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SORT1 MUTATED       0                         1     4
  SORT1 WILD-TYPE     9                         4   124
D100V14, multiclass
                           clus
vv                          SORT1 MUTATED SORT1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V15, binary
                 cls
clus                0   1
  SORT1 MUTATED     0   5
  SORT1 WILD-TYPE   5 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SORT1 MUTATED      0    5
  SORT1 WILD-TYPE    5  100
                        clus
vv                       SORT1 MUTATED SORT1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             100
[1] 2 2
[1] FALSE

Clustering(101) Variable = NBPF9 MUTATION ANALYSIS
D101V1, survival
                 sevent
clus2              0  1
  NBPF9 MUTATED    2  1
  NBPF9 WILD-TYPE 66 75
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              3             141 
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              1              75 
$`NBPF9 MUTATED`
TCGA-2L-AAQI TCGA-HV-AA8V TCGA-XN-A8T5 
        3.39        30.25        23.67 

$`NBPF9 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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
        8.28        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A8RO 
       13.68         3.12        15.32         9.40        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-YB-A89D 
       13.81        12.99        12.03        16.37        31.27        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  NBPF9 MUTATED NBPF9 WILD-TYPE 
           3.39            0.03 
  NBPF9 MUTATED NBPF9 WILD-TYPE 
          30.25           75.12 
  NBPF9 MUTATED NBPF9 WILD-TYPE 
          23.67           14.17 
[1] "3.4 - 30.2 (23.7)" "0.0 - 75.1 (14.2)"
[1] "hr=" "2.2"
D101V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NBPF9 MUTATED          0        1         0         2         0        0
  NBPF9 WILD-TYPE        3        7        23       101         4        4
D101V3, multiclass
           clus
vv          NBPF9 MUTATED NBPF9 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             0              23
  STAGE IIB             2             101
  STAGE III             0               4
  STAGE IV              0               4
[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
  NBPF9 MUTATED     0   1     2
  NBPF9 WILD-TYPE   4  15   123
D101V4, multiclass
       clus
vv      NBPF9 MUTATED NBPF9 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D101V5, binary
                 cls
clus                0   1
  NBPF9 MUTATED     1   2
  NBPF9 WILD-TYPE  36 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      1    2
  NBPF9 WILD-TYPE   36  106
   clus
vv  NBPF9 MUTATED NBPF9 WILD-TYPE
  0             1              36
  1             2             106
[1] 2 2
[1] FALSE
D101V6, binary
                 cls
clus               0  1
  NBPF9 MUTATED    1  0
  NBPF9 WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      1    0
  NBPF9 WILD-TYPE   65    4
   clus
vv  NBPF9 MUTATED NBPF9 WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D101V7, binary
                 cls
clus               0  1
  NBPF9 MUTATED    1  2
  NBPF9 WILD-TYPE 66 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      1    2
  NBPF9 WILD-TYPE   66   77
        clus
vv       NBPF9 MUTATED NBPF9 WILD-TYPE
  FEMALE             1              66
  MALE               2              77
[1] 2 2
[1] FALSE
D101V8, binary
                 cls
clus               0  1
  NBPF9 MUTATED    2  1
  NBPF9 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      2    1
  NBPF9 WILD-TYPE   92   35
     clus
vv    NBPF9 MUTATED NBPF9 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NBPF9 MUTATED                                     2
  NBPF9 WILD-TYPE                                 128
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NBPF9 MUTATED                                       1
  NBPF9 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NBPF9 MUTATED                                                  0
  NBPF9 WILD-TYPE                                                2
D101V9, multiclass
                                                  clus
vv                                                 NBPF9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NBPF9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D101V10, continuous
[1] "Remove cluster labels:" "NBPF9 MUTATED"         
clus
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              2              48 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-IB-7644 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-7886 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
D101V11, continuous
[1] "Remove cluster labels:" "NBPF9 MUTATED"         
clus
  NBPF9 MUTATED NBPF9 WILD-TYPE 
              1              39 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
     TCGA-XD-AAUI      TCGA-XD-AAUL      TCGA-YY-A8LH 
"NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" "NBPF9 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NBPF9 MUTATED    0  2  1  0
  NBPF9 WILD-TYPE 79 48  3  3
D101V12, multiclass
    clus
vv   NBPF9 MUTATED NBPF9 WILD-TYPE
  R0             0              79
  R1             2              48
  R2             1               3
  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"
D101V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF9 MUTATED       1                         0     2
  NBPF9 WILD-TYPE     8                         5   126
D101V14, multiclass
                           clus
vv                          NBPF9 MUTATED NBPF9 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 2             126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V15, binary
                 cls
clus                0   1
  NBPF9 MUTATED     1   0
  NBPF9 WILD-TYPE   4 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF9 MUTATED      1    0
  NBPF9 WILD-TYPE    4  105
                        clus
vv                       NBPF9 MUTATED NBPF9 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             0             105
[1] 2 2
[1] FALSE

Clustering(102) Variable = C5ORF51 MUTATION ANALYSIS
D102V1, survival
                   sevent
clus2                0  1
  C5ORF51 MUTATED    1  2
  C5ORF51 WILD-TYPE 67 74
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                3               141 
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                2                74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
       20.19        17.03        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
             3.95              0.03 
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
            41.33             75.12 
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
            19.82             14.17 
[1] "4.0 - 41.3 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1"  
D102V2, 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        3        8        23       100         4        4
D102V3, multiclass
           clus
vv          C5ORF51 MUTATED C5ORF51 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               0                23
  STAGE IIB               3               100
  STAGE III               0                 4
  STAGE IV                0                 4
[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   4  16   122
D102V4, multiclass
       clus
vv      C5ORF51 MUTATED C5ORF51 WILD-TYPE
  T1                  0                 4
  T2                  0                16
  T3+T4               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"
D102V5, binary
                   cls
clus                  0   1
  C5ORF51 MUTATED     0   3
  C5ORF51 WILD-TYPE  37 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF51 MUTATED      0    3
  C5ORF51 WILD-TYPE   37  105
   clus
vv  C5ORF51 MUTATED C5ORF51 WILD-TYPE
  0               0                37
  1               3               105
[1] 2 2
[1] FALSE
D102V6, binary
                   cls
clus                 0  1
  C5ORF51 MUTATED    2  0
  C5ORF51 WILD-TYPE 64  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF51 MUTATED      2    0
  C5ORF51 WILD-TYPE   64    4
   clus
vv  C5ORF51 MUTATED C5ORF51 WILD-TYPE
  0               2                64
  1               0                 4
[1] 2 2
[1] FALSE
D102V7, binary
                   cls
clus                 0  1
  C5ORF51 MUTATED    2  1
  C5ORF51 WILD-TYPE 65 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF51 MUTATED      2    1
  C5ORF51 WILD-TYPE   65   78
        clus
vv       C5ORF51 MUTATED C5ORF51 WILD-TYPE
  FEMALE               2                65
  MALE                 1                78
[1] 2 2
[1] FALSE
D102V8, binary
                   cls
clus                 0  1
  C5ORF51 MUTATED    3  0
  C5ORF51 WILD-TYPE 91 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF51 MUTATED      3    0
  C5ORF51 WILD-TYPE   91   36
     clus
vv    C5ORF51 MUTATED C5ORF51 WILD-TYPE
  NO                3                91
  YES               0                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C5ORF51 MUTATED                                     3
  C5ORF51 WILD-TYPE                                 127
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C5ORF51 MUTATED                                       0
  C5ORF51 WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C5ORF51 MUTATED                                                  0
  C5ORF51 WILD-TYPE                                                2
D102V9, 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                            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D102V10, continuous
[1] "Remove cluster labels:" "C5ORF51 MUTATED"       
clus
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                2                48 
       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-HV-AA8V        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-7887 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
D102V11, continuous
[1] "Remove cluster labels:" "C5ORF51 MUTATED"       
clus
  C5ORF51 MUTATED C5ORF51 WILD-TYPE 
                2                38 
       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-XN-A8T5        TCGA-YY-A8LH 
"C5ORF51 WILD-TYPE" "C5ORF51 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  C5ORF51 MUTATED    2  1  0  0
  C5ORF51 WILD-TYPE 77 49  4  3
D102V12, multiclass
    clus
vv   C5ORF51 MUTATED C5ORF51 WILD-TYPE
  R0               2                77
  R1               1                49
  R2               0                 4
  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"
D102V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C5ORF51 MUTATED       0                         0     3
  C5ORF51 WILD-TYPE     9                         5   125
D102V14, multiclass
                           clus
vv                          C5ORF51 MUTATED C5ORF51 WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V15, binary
                   cls
clus                  0   1
  C5ORF51 MUTATED     0   3
  C5ORF51 WILD-TYPE   5 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF51 MUTATED      0    3
  C5ORF51 WILD-TYPE    5  102
                        clus
vv                       C5ORF51 MUTATED C5ORF51 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3               102
[1] 2 2
[1] FALSE

Clustering(103) Variable = CSTF2T MUTATION ANALYSIS
D103V1, survival
                  sevent
clus2               0  1
  CSTF2T MUTATED    1  2
  CSTF2T WILD-TYPE 67 74
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               3              141 
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               2               74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       19.82        23.80        41.33         4.04         3.62        43.79 
TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-8126 TCGA-IB-8127 
       15.81        19.66        21.30         3.85         2.47        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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  CSTF2T MUTATED CSTF2T WILD-TYPE 
           15.98             0.03 
  CSTF2T MUTATED CSTF2T WILD-TYPE 
           21.90            75.12 
  CSTF2T MUTATED CSTF2T WILD-TYPE 
           20.19            14.14 
[1] "16.0 - 21.9 (20.2)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "1.1"
D103V2, 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        3        8        23       100         4        4
D103V3, multiclass
           clus
vv          CSTF2T MUTATED CSTF2T WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   122
D103V4, multiclass
       clus
vv      CSTF2T MUTATED CSTF2T WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D103V5, binary
                  cls
clus                 0   1
  CSTF2T MUTATED     0   3
  CSTF2T WILD-TYPE  37 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSTF2T MUTATED      0    3
  CSTF2T WILD-TYPE   37  105
   clus
vv  CSTF2T MUTATED CSTF2T WILD-TYPE
  0              0               37
  1              3              105
[1] 2 2
[1] FALSE
D103V6, binary
                  cls
clus                0  1
  CSTF2T MUTATED    2  0
  CSTF2T WILD-TYPE 64  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSTF2T MUTATED      2    0
  CSTF2T WILD-TYPE   64    4
   clus
vv  CSTF2T MUTATED CSTF2T WILD-TYPE
  0              2               64
  1              0                4
[1] 2 2
[1] FALSE
D103V7, binary
                  cls
clus                0  1
  CSTF2T MUTATED    1  2
  CSTF2T WILD-TYPE 66 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSTF2T MUTATED      1    2
  CSTF2T WILD-TYPE   66   77
        clus
vv       CSTF2T MUTATED CSTF2T WILD-TYPE
  FEMALE              1               66
  MALE                2               77
[1] 2 2
[1] FALSE
D103V8, binary
                  cls
clus                0  1
  CSTF2T MUTATED    3  0
  CSTF2T WILD-TYPE 91 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSTF2T MUTATED      3    0
  CSTF2T WILD-TYPE   91   36
     clus
vv    CSTF2T MUTATED CSTF2T WILD-TYPE
  NO               3               91
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CSTF2T MUTATED                                     3
  CSTF2T WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CSTF2T MUTATED                                       0
  CSTF2T WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CSTF2T MUTATED                                                  0
  CSTF2T WILD-TYPE                                                2
D103V9, 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                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D103V10, continuous
[1] "Remove cluster labels:" "CSTF2T MUTATED"        
clus
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               1               49 
      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-HV-AA8V       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-7887       TCGA-IB-7891       TCGA-IB-8126 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-8127       TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-IB-A7M4 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-S4-A8RP       TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
      TCGA-YY-A8LH 
"CSTF2T WILD-TYPE" 
D103V11, continuous
[1] "Remove cluster labels:" "CSTF2T MUTATED"        
clus
  CSTF2T MUTATED CSTF2T WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" "CSTF2T WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CSTF2T MUTATED    2  1  0  0
  CSTF2T WILD-TYPE 77 49  4  3
D103V12, multiclass
    clus
vv   CSTF2T MUTATED CSTF2T WILD-TYPE
  R0              2               77
  R1              1               49
  R2              0                4
  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"
D103V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSTF2T MUTATED       0                         0     3
  CSTF2T WILD-TYPE     9                         5   125
D103V14, multiclass
                           clus
vv                          CSTF2T MUTATED CSTF2T WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V15, binary
                  cls
clus                 0   1
  CSTF2T MUTATED     0   3
  CSTF2T WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSTF2T MUTATED      0    3
  CSTF2T WILD-TYPE    5  102
                        clus
vv                       CSTF2T MUTATED CSTF2T WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(104) Variable = SSBP3 MUTATION ANALYSIS
D104V1, survival
                 sevent
clus2              0  1
  SSBP3 MUTATED    0  3
  SSBP3 WILD-TYPE 68 73
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3             141 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       19.82        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-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UF 
       17.16        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-PZ-A5RE TCGA-Q3-A5QY 
       12.92        12.46        10.29        19.20        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SSBP3 MUTATED SSBP3 WILD-TYPE 
           5.03            0.03 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
          12.00           75.12 
  SSBP3 MUTATED SSBP3 WILD-TYPE 
           8.78           14.47 
[1] "5.0 - 12.0 (8.8)"  "0.0 - 75.1 (14.5)"
[1] "hr=" "5.2"
D104V2, 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        3        8        22       101         4        4
D104V3, multiclass
           clus
vv          SSBP3 MUTATED SSBP3 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             2             101
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D104V4, multiclass
       clus
vv      SSBP3 MUTATED SSBP3 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D104V5, binary
                 cls
clus                0   1
  SSBP3 MUTATED     1   2
  SSBP3 WILD-TYPE  36 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      1    2
  SSBP3 WILD-TYPE   36  106
   clus
vv  SSBP3 MUTATED SSBP3 WILD-TYPE
  0             1              36
  1             2             106
[1] 2 2
[1] FALSE
D104V6, binary
                 cls
clus               0  1
  SSBP3 MUTATED    2  0
  SSBP3 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      2    0
  SSBP3 WILD-TYPE   64    4
   clus
vv  SSBP3 MUTATED SSBP3 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D104V7, binary
                 cls
clus               0  1
  SSBP3 MUTATED    1  2
  SSBP3 WILD-TYPE 66 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      1    2
  SSBP3 WILD-TYPE   66   77
        clus
vv       SSBP3 MUTATED SSBP3 WILD-TYPE
  FEMALE             1              66
  MALE               2              77
[1] 2 2
[1] FALSE
D104V8, binary
                 cls
clus               0  1
  SSBP3 MUTATED    2  1
  SSBP3 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      2    1
  SSBP3 WILD-TYPE   92   35
     clus
vv    SSBP3 MUTATED SSBP3 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SSBP3 MUTATED                                     3
  SSBP3 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SSBP3 MUTATED                                       0
  SSBP3 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SSBP3 MUTATED                                                  0
  SSBP3 WILD-TYPE                                                2
D104V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D104V10, continuous
[1] "Remove cluster labels:" "SSBP3 MUTATED"         
clus
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-S4-A8RM 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
     TCGA-YY-A8LH 
"SSBP3 WILD-TYPE" 
D104V11, continuous
[1] "Remove cluster labels:" "SSBP3 MUTATED"         
clus
  SSBP3 MUTATED SSBP3 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" "SSBP3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SSBP3 MUTATED    2  1  0  0
  SSBP3 WILD-TYPE 77 49  4  3
D104V12, multiclass
    clus
vv   SSBP3 MUTATED SSBP3 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D104V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SSBP3 MUTATED       0                         0     3
  SSBP3 WILD-TYPE     9                         5   125
D104V14, multiclass
                           clus
vv                          SSBP3 MUTATED SSBP3 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V15, binary
                 cls
clus                0   1
  SSBP3 MUTATED     0   2
  SSBP3 WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSBP3 MUTATED      0    2
  SSBP3 WILD-TYPE    5  103
                        clus
vv                       SSBP3 MUTATED SSBP3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(105) Variable = PRSS3 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2              0  1
  PRSS3 MUTATED    0  3
  PRSS3 WILD-TYPE 68 73
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              3             141 
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              3              73 
$`PRSS3 MUTATED`
TCGA-3A-A9IU TCGA-FB-A5VM TCGA-LB-A9Q5 
       15.06        16.37        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       33.57        34.09        10.13        24.43        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        12.66         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  PRSS3 MUTATED PRSS3 WILD-TYPE 
          10.29            0.03 
  PRSS3 MUTATED PRSS3 WILD-TYPE 
          16.37           75.12 
  PRSS3 MUTATED PRSS3 WILD-TYPE 
          15.06           14.17 
[1] "10.3 - 16.4 (15.1)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "2.5"
D105V2, 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        3        7        23       101         4        4
D105V3, multiclass
           clus
vv          PRSS3 MUTATED PRSS3 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             0              23
  STAGE IIB             2             101
  STAGE III             0               4
  STAGE IV              0               4
[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   4  15   123
D105V4, multiclass
       clus
vv      PRSS3 MUTATED PRSS3 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D105V5, binary
                 cls
clus                0   1
  PRSS3 MUTATED     1   2
  PRSS3 WILD-TYPE  36 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      1    2
  PRSS3 WILD-TYPE   36  106
   clus
vv  PRSS3 MUTATED PRSS3 WILD-TYPE
  0             1              36
  1             2             106
[1] 2 2
[1] FALSE
D105V6, binary
                 cls
clus               0  1
  PRSS3 MUTATED    1  0
  PRSS3 WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      1    0
  PRSS3 WILD-TYPE   65    4
   clus
vv  PRSS3 MUTATED PRSS3 WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D105V7, binary
                 cls
clus               0  1
  PRSS3 MUTATED    1  2
  PRSS3 WILD-TYPE 66 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      1    2
  PRSS3 WILD-TYPE   66   77
        clus
vv       PRSS3 MUTATED PRSS3 WILD-TYPE
  FEMALE             1              66
  MALE               2              77
[1] 2 2
[1] FALSE
D105V8, binary
                 cls
clus               0  1
  PRSS3 MUTATED    2  1
  PRSS3 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      2    1
  PRSS3 WILD-TYPE   92   35
     clus
vv    PRSS3 MUTATED PRSS3 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PRSS3 MUTATED                                     3
  PRSS3 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PRSS3 MUTATED                                       0
  PRSS3 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PRSS3 MUTATED                                                  0
  PRSS3 WILD-TYPE                                                2
D105V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D105V10, continuous
[1] "Remove cluster labels:" "PRSS3 MUTATED"         
clus
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              2              48 
     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-HV-AA8V 
"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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
D105V11, continuous
[1] "Remove cluster labels:" "PRSS3 MUTATED"         
clus
  PRSS3 MUTATED PRSS3 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"PRSS3 WILD-TYPE" "PRSS3 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PRSS3 MUTATED    3  0  0  0
  PRSS3 WILD-TYPE 76 50  4  3
D105V12, multiclass
    clus
vv   PRSS3 MUTATED PRSS3 WILD-TYPE
  R0             3              76
  R1             0              50
  R2             0               4
  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"
D105V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRSS3 MUTATED       0                         0     3
  PRSS3 WILD-TYPE     9                         5   125
D105V14, multiclass
                           clus
vv                          PRSS3 MUTATED PRSS3 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V15, binary
                 cls
clus                0   1
  PRSS3 MUTATED     0   3
  PRSS3 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRSS3 MUTATED      0    3
  PRSS3 WILD-TYPE    5  102
                        clus
vv                       PRSS3 MUTATED PRSS3 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(106) Variable = UBXN4 MUTATION ANALYSIS
D106V1, survival
                 sevent
clus2              0  1
  UBXN4 MUTATED    0  3
  UBXN4 WILD-TYPE 68 73
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              3             141 
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  UBXN4 MUTATED UBXN4 WILD-TYPE 
           3.62            0.03 
  UBXN4 MUTATED UBXN4 WILD-TYPE 
          20.19           75.12 
  UBXN4 MUTATED UBXN4 WILD-TYPE 
          19.82           14.17 
[1] "3.6 - 20.2 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "2"  
D106V2, 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        3        8        23       100         4        4
D106V3, multiclass
           clus
vv          UBXN4 MUTATED UBXN4 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D106V4, multiclass
       clus
vv      UBXN4 MUTATED UBXN4 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D106V5, binary
                 cls
clus                0   1
  UBXN4 MUTATED     0   3
  UBXN4 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN4 MUTATED      0    3
  UBXN4 WILD-TYPE   37  105
   clus
vv  UBXN4 MUTATED UBXN4 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D106V6, binary
                 cls
clus               0  1
  UBXN4 MUTATED    2  0
  UBXN4 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN4 MUTATED      2    0
  UBXN4 WILD-TYPE   64    4
   clus
vv  UBXN4 MUTATED UBXN4 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D106V7, binary
                 cls
clus               0  1
  UBXN4 MUTATED    2  1
  UBXN4 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN4 MUTATED      2    1
  UBXN4 WILD-TYPE   65   78
        clus
vv       UBXN4 MUTATED UBXN4 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D106V8, binary
                 cls
clus               0  1
  UBXN4 MUTATED    3  0
  UBXN4 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN4 MUTATED      3    0
  UBXN4 WILD-TYPE   91   36
     clus
vv    UBXN4 MUTATED UBXN4 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UBXN4 MUTATED                                     3
  UBXN4 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UBXN4 MUTATED                                       0
  UBXN4 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UBXN4 MUTATED                                                  0
  UBXN4 WILD-TYPE                                                2
D106V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D106V10, continuous
[1] "Remove cluster labels:" "UBXN4 MUTATED"         
clus
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-IB-AAUU      TCGA-LB-A7SX 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
D106V11, continuous
[1] "Remove cluster labels:" "UBXN4 MUTATED"         
clus
  UBXN4 MUTATED UBXN4 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" "UBXN4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  UBXN4 MUTATED    2  1  0  0
  UBXN4 WILD-TYPE 77 49  4  3
D106V12, multiclass
    clus
vv   UBXN4 MUTATED UBXN4 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D106V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBXN4 MUTATED       0                         0     3
  UBXN4 WILD-TYPE     9                         5   125
D106V14, multiclass
                           clus
vv                          UBXN4 MUTATED UBXN4 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V15, binary
                 cls
clus                0   1
  UBXN4 MUTATED     0   3
  UBXN4 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN4 MUTATED      0    3
  UBXN4 WILD-TYPE    5  102
                        clus
vv                       UBXN4 MUTATED UBXN4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(107) Variable = AGAP6 MUTATION ANALYSIS
D107V1, survival
                 sevent
clus2              0  1
  AGAP6 MUTATED    4  3
  AGAP6 WILD-TYPE 64 73
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              7             137 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              3              73 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 
        6.38        10.85         1.08         0.23        19.82        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-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ 
        3.85        15.98         2.47        12.00        15.85         7.20 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-IB-AAUM TCGA-IB-AAUN 
       20.88         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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
        0.39        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  AGAP6 MUTATED AGAP6 WILD-TYPE 
           5.26            0.03 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          21.90           75.12 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          17.16           13.84 
[1] "5.3 - 21.9 (17.2)" "0.0 - 75.1 (13.8)"
[1] "hr=" "1.4"
D107V2, 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        3        8        22        97         4        4
D107V3, multiclass
           clus
vv          AGAP6 MUTATED AGAP6 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             6              97
  STAGE III             0               4
  STAGE IV              0               4
[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   4  15   119
D107V4, multiclass
       clus
vv      AGAP6 MUTATED AGAP6 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D107V5, binary
                 cls
clus                0   1
  AGAP6 MUTATED     1   6
  AGAP6 WILD-TYPE  36 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      1    6
  AGAP6 WILD-TYPE   36  102
   clus
vv  AGAP6 MUTATED AGAP6 WILD-TYPE
  0             1              36
  1             6             102
[1] 2 2
[1] FALSE
D107V6, binary
                 cls
clus               0  1
  AGAP6 MUTATED    5  0
  AGAP6 WILD-TYPE 61  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      5    0
  AGAP6 WILD-TYPE   61    4
   clus
vv  AGAP6 MUTATED AGAP6 WILD-TYPE
  0             5              61
  1             0               4
[1] 2 2
[1] FALSE
D107V7, binary
                 cls
clus               0  1
  AGAP6 MUTATED    4  3
  AGAP6 WILD-TYPE 63 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      4    3
  AGAP6 WILD-TYPE   63   76
        clus
vv       AGAP6 MUTATED AGAP6 WILD-TYPE
  FEMALE             4              63
  MALE               3              76
[1] 2 2
[1] FALSE
D107V8, binary
                 cls
clus               0  1
  AGAP6 MUTATED    6  1
  AGAP6 WILD-TYPE 88 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      6    1
  AGAP6 WILD-TYPE   88   35
     clus
vv    AGAP6 MUTATED AGAP6 WILD-TYPE
  NO              6              88
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AGAP6 MUTATED                                     6
  AGAP6 WILD-TYPE                                 124
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AGAP6 MUTATED                                       1
  AGAP6 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AGAP6 MUTATED                                                  0
  AGAP6 WILD-TYPE                                                2
D107V9, 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                          124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D107V10, continuous
D107V11, continuous
                 vv
clus              R0 R1 R2 RX
  AGAP6 MUTATED    4  3  0  0
  AGAP6 WILD-TYPE 75 47  4  3
D107V12, multiclass
    clus
vv   AGAP6 MUTATED AGAP6 WILD-TYPE
  R0             4              75
  R1             3              47
  R2             0               4
  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"
D107V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AGAP6 MUTATED       0                         0     7
  AGAP6 WILD-TYPE     9                         5   121
D107V14, multiclass
                           clus
vv                          AGAP6 MUTATED AGAP6 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             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"
D107V15, binary
                 cls
clus               0  1
  AGAP6 MUTATED    0  6
  AGAP6 WILD-TYPE  5 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      0    6
  AGAP6 WILD-TYPE    5   99
                        clus
vv                       AGAP6 MUTATED AGAP6 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              99
[1] 2 2
[1] FALSE

Clustering(108) Variable = TGM5 MUTATION ANALYSIS
D108V1, survival
                sevent
clus2             0  1
  TGM5 MUTATED    2  2
  TGM5 WILD-TYPE 66 74
  TGM5 MUTATED TGM5 WILD-TYPE 
             4            140 
  TGM5 MUTATED TGM5 WILD-TYPE 
             2             74 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-AA2A 
       12.46        10.29        19.20         8.78        15.45         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TGM5 MUTATED TGM5 WILD-TYPE 
          2.47           0.03 
  TGM5 MUTATED TGM5 WILD-TYPE 
         13.68          75.12 
  TGM5 MUTATED TGM5 WILD-TYPE 
         12.69          14.70 
[1] "2.5 - 13.7 (12.7)" "0.0 - 75.1 (14.7)"
[1] "hr=" "1.8"
D108V2, 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        3        8        23       101         2        4
D108V3, multiclass
           clus
vv          TGM5 MUTATED TGM5 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            2            101
  STAGE III            2              2
  STAGE IV             0              4
[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   4  16   121
D108V4, multiclass
       clus
vv      TGM5 MUTATED TGM5 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D108V5, binary
                cls
clus               0   1
  TGM5 MUTATED     1   3
  TGM5 WILD-TYPE  36 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM5 MUTATED      1    3
  TGM5 WILD-TYPE   36  105
   clus
vv  TGM5 MUTATED TGM5 WILD-TYPE
  0            1             36
  1            3            105
[1] 2 2
[1] FALSE
D108V6, binary
                cls
clus              0  1
  TGM5 MUTATED    1  0
  TGM5 WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM5 MUTATED      1    0
  TGM5 WILD-TYPE   65    4
   clus
vv  TGM5 MUTATED TGM5 WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D108V7, binary
                cls
clus              0  1
  TGM5 MUTATED    3  1
  TGM5 WILD-TYPE 64 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM5 MUTATED      3    1
  TGM5 WILD-TYPE   64   78
        clus
vv       TGM5 MUTATED TGM5 WILD-TYPE
  FEMALE            3             64
  MALE              1             78
[1] 2 2
[1] FALSE
D108V8, binary
                cls
clus              0  1
  TGM5 MUTATED    2  1
  TGM5 WILD-TYPE 92 35
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM5 MUTATED      2    1
  TGM5 WILD-TYPE   92   35
     clus
vv    TGM5 MUTATED TGM5 WILD-TYPE
  NO             2             92
  YES            1             35
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGM5 MUTATED                                     4
  TGM5 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGM5 MUTATED                                       0
  TGM5 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGM5 MUTATED                                                  0
  TGM5 WILD-TYPE                                                2
D108V9, multiclass
                                                  clus
vv                                                 TGM5 MUTATED TGM5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D108V10, continuous
[1] "Remove cluster labels:" "TGM5 MUTATED"          
clus
  TGM5 MUTATED TGM5 WILD-TYPE 
             1             49 
    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-HV-AA8V     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-7887     TCGA-IB-7891     TCGA-IB-8127 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
    TCGA-YY-A8LH 
"TGM5 WILD-TYPE" 
D108V11, continuous
[1] "Remove cluster labels:" "TGM5 MUTATED"          
clus
  TGM5 MUTATED TGM5 WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"TGM5 WILD-TYPE" "TGM5 WILD-TYPE" "TGM5 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  TGM5 MUTATED    1  3  0  0
  TGM5 WILD-TYPE 78 47  4  3
D108V12, multiclass
    clus
vv   TGM5 MUTATED TGM5 WILD-TYPE
  R0            1             78
  R1            3             47
  R2            0              4
  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"
D108V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGM5 MUTATED       0                         0     4
  TGM5 WILD-TYPE     9                         5   124
D108V14, multiclass
                           clus
vv                          TGM5 MUTATED TGM5 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V15, binary
                cls
clus               0   1
  TGM5 MUTATED     0   3
  TGM5 WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  TGM5 MUTATED      0    3
  TGM5 WILD-TYPE    5  102
                        clus
vv                       TGM5 MUTATED TGM5 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(109) Variable = GPRC6A MUTATION ANALYSIS
D109V1, survival
                  sevent
clus2               0  1
  GPRC6A MUTATED    2  3
  GPRC6A WILD-TYPE 66 73
  GPRC6A MUTATED GPRC6A WILD-TYPE 
               5              139 
  GPRC6A MUTATED GPRC6A WILD-TYPE 
               3               73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  GPRC6A MUTATED GPRC6A WILD-TYPE 
           15.35             0.03 
  GPRC6A MUTATED GPRC6A WILD-TYPE 
           71.74            75.12 
  GPRC6A MUTATED GPRC6A WILD-TYPE 
           23.21            13.84 
[1] "15.3 - 71.7 (23.2)" "0.0 - 75.1 (13.8)" 
[1] "hr=" "2.1"
D109V2, 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        3        8        22       100         3        4
D109V3, multiclass
           clus
vv          GPRC6A MUTATED GPRC6A WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              3              100
  STAGE III              1                3
  STAGE IV               0                4
[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   4  16   120
D109V4, multiclass
       clus
vv      GPRC6A MUTATED GPRC6A WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D109V5, binary
                  cls
clus                 0   1
  GPRC6A MUTATED     2   3
  GPRC6A WILD-TYPE  35 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRC6A MUTATED      2    3
  GPRC6A WILD-TYPE   35  105
   clus
vv  GPRC6A MUTATED GPRC6A WILD-TYPE
  0              2               35
  1              3              105
[1] 2 2
[1] FALSE
D109V6, binary
                  cls
clus                0  1
  GPRC6A MUTATED    3  0
  GPRC6A WILD-TYPE 63  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRC6A MUTATED      3    0
  GPRC6A WILD-TYPE   63    4
   clus
vv  GPRC6A MUTATED GPRC6A WILD-TYPE
  0              3               63
  1              0                4
[1] 2 2
[1] FALSE
D109V7, binary
                  cls
clus                0  1
  GPRC6A MUTATED    3  2
  GPRC6A WILD-TYPE 64 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRC6A MUTATED      3    2
  GPRC6A WILD-TYPE   64   77
        clus
vv       GPRC6A MUTATED GPRC6A WILD-TYPE
  FEMALE              3               64
  MALE                2               77
[1] 2 2
[1] FALSE
D109V8, binary
                  cls
clus                0  1
  GPRC6A MUTATED    4  0
  GPRC6A WILD-TYPE 90 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRC6A MUTATED      4    0
  GPRC6A WILD-TYPE   90   36
     clus
vv    GPRC6A MUTATED GPRC6A WILD-TYPE
  NO               4               90
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPRC6A MUTATED                                     5
  GPRC6A WILD-TYPE                                 125
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPRC6A MUTATED                                       0
  GPRC6A WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPRC6A MUTATED                                                  0
  GPRC6A WILD-TYPE                                                2
D109V9, 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                           125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D109V10, continuous
D109V11, continuous
                  vv
clus               R0 R1 R2 RX
  GPRC6A MUTATED    3  1  0  0
  GPRC6A WILD-TYPE 76 49  4  3
D109V12, multiclass
    clus
vv   GPRC6A MUTATED GPRC6A WILD-TYPE
  R0              3               76
  R1              1               49
  R2              0                4
  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"
D109V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPRC6A MUTATED       0                         0     4
  GPRC6A WILD-TYPE     9                         5   124
D109V14, multiclass
                           clus
vv                          GPRC6A MUTATED GPRC6A WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V15, binary
                  cls
clus                 0   1
  GPRC6A MUTATED     1   3
  GPRC6A WILD-TYPE   4 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRC6A MUTATED      1    3
  GPRC6A WILD-TYPE    4  102
                        clus
vv                       GPRC6A MUTATED GPRC6A WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(110) Variable = OR52D1 MUTATION ANALYSIS
D110V1, survival
                  sevent
clus2               0  1
  OR52D1 MUTATED    3  1
  OR52D1 WILD-TYPE 65 75
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               4              140 
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               1               75 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       12.43        17.92        21.70        16.14        10.13         6.38 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  OR52D1 MUTATED OR52D1 WILD-TYPE 
           11.93             0.03 
  OR52D1 MUTATED OR52D1 WILD-TYPE 
           21.60            75.12 
  OR52D1 MUTATED OR52D1 WILD-TYPE 
          17.375           14.155 
[1] "11.9 - 21.6 (17.4)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "2.3"
D110V2, 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        2        8        23       100         4        4
D110V3, multiclass
           clus
vv          OR52D1 MUTATED OR52D1 WILD-TYPE
  STAGE IA               1                2
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   3  16   122
D110V4, multiclass
       clus
vv      OR52D1 MUTATED OR52D1 WILD-TYPE
  T1                 1                3
  T2                 0               16
  T3+T4              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"
D110V5, binary
                  cls
clus                 0   1
  OR52D1 MUTATED     1   3
  OR52D1 WILD-TYPE  36 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52D1 MUTATED      1    3
  OR52D1 WILD-TYPE   36  105
   clus
vv  OR52D1 MUTATED OR52D1 WILD-TYPE
  0              1               36
  1              3              105
[1] 2 2
[1] FALSE
D110V6, binary
                  cls
clus                0  1
  OR52D1 MUTATED    1  0
  OR52D1 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52D1 MUTATED      1    0
  OR52D1 WILD-TYPE   65    4
   clus
vv  OR52D1 MUTATED OR52D1 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D110V7, binary
                  cls
clus                0  1
  OR52D1 MUTATED    1  3
  OR52D1 WILD-TYPE 66 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52D1 MUTATED      1    3
  OR52D1 WILD-TYPE   66   76
        clus
vv       OR52D1 MUTATED OR52D1 WILD-TYPE
  FEMALE              1               66
  MALE                3               76
[1] 2 2
[1] FALSE
D110V8, binary
                  cls
clus                0  1
  OR52D1 MUTATED    1  3
  OR52D1 WILD-TYPE 93 33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52D1 MUTATED      1    3
  OR52D1 WILD-TYPE   93   33
     clus
vv    OR52D1 MUTATED OR52D1 WILD-TYPE
  NO               1               93
  YES              3               33
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR52D1 MUTATED                                     2
  OR52D1 WILD-TYPE                                 128
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR52D1 MUTATED                                       2
  OR52D1 WILD-TYPE                                    11
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR52D1 MUTATED                                                  0
  OR52D1 WILD-TYPE                                                2
D110V9, 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                           128
  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"
D110V10, continuous
[1] "Remove cluster labels:" "OR52D1 MUTATED"        
clus
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               2               48 
      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-HV-AA8V 
"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-7887 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
D110V11, continuous
[1] "Remove cluster labels:" "OR52D1 MUTATED"        
clus
  OR52D1 MUTATED OR52D1 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"OR52D1 WILD-TYPE" "OR52D1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  OR52D1 MUTATED    2  1  0  0
  OR52D1 WILD-TYPE 77 49  4  3
D110V12, multiclass
    clus
vv   OR52D1 MUTATED OR52D1 WILD-TYPE
  R0              2               77
  R1              1               49
  R2              0                4
  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"
D110V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR52D1 MUTATED       0                         0     4
  OR52D1 WILD-TYPE     9                         5   124
D110V14, multiclass
                           clus
vv                          OR52D1 MUTATED OR52D1 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V15, binary
                  cls
clus                 0   1
  OR52D1 MUTATED     0   4
  OR52D1 WILD-TYPE   5 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52D1 MUTATED      0    4
  OR52D1 WILD-TYPE    5  101
                        clus
vv                       OR52D1 MUTATED OR52D1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              101
[1] 2 2
[1] FALSE

Clustering(111) Variable = KLK13 MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2              0  1
  KLK13 MUTATED    2  3
  KLK13 WILD-TYPE 66 73
  KLK13 MUTATED KLK13 WILD-TYPE 
              5             139 
  KLK13 MUTATED KLK13 WILD-TYPE 
              3              73 
$`KLK13 MUTATED`
TCGA-2L-AAQE TCGA-FB-A78T TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-A5SS 
       22.49         0.03         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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
       21.60         5.26        10.85         0.23        19.82        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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  KLK13 MUTATED KLK13 WILD-TYPE 
           0.03            0.13 
  KLK13 MUTATED KLK13 WILD-TYPE 
          22.49           75.12 
  KLK13 MUTATED KLK13 WILD-TYPE 
          15.12           14.17 
[1] "0.0 - 22.5 (15.1)" "0.1 - 75.1 (14.2)"
[1] "hr=" "1.5"
D111V2, 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        3        8        23        98         4        4
D111V3, multiclass
           clus
vv          KLK13 MUTATED KLK13 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   120
D111V4, multiclass
       clus
vv      KLK13 MUTATED KLK13 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D111V5, binary
                 cls
clus                0   1
  KLK13 MUTATED     0   5
  KLK13 WILD-TYPE  37 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      0    5
  KLK13 WILD-TYPE   37  103
   clus
vv  KLK13 MUTATED KLK13 WILD-TYPE
  0             0              37
  1             5             103
[1] 2 2
[1] FALSE
D111V6, binary
                 cls
clus               0  1
  KLK13 MUTATED    4  0
  KLK13 WILD-TYPE 62  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      4    0
  KLK13 WILD-TYPE   62    4
   clus
vv  KLK13 MUTATED KLK13 WILD-TYPE
  0             4              62
  1             0               4
[1] 2 2
[1] FALSE
D111V7, binary
                 cls
clus               0  1
  KLK13 MUTATED    4  1
  KLK13 WILD-TYPE 63 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      4    1
  KLK13 WILD-TYPE   63   78
        clus
vv       KLK13 MUTATED KLK13 WILD-TYPE
  FEMALE             4              63
  MALE               1              78
[1] 2 2
[1] FALSE
D111V8, binary
                 cls
clus               0  1
  KLK13 MUTATED    3  0
  KLK13 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      3    0
  KLK13 WILD-TYPE   91   36
     clus
vv    KLK13 MUTATED KLK13 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KLK13 MUTATED                                     4
  KLK13 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KLK13 MUTATED                                       1
  KLK13 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KLK13 MUTATED                                                  0
  KLK13 WILD-TYPE                                                2
D111V9, 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                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D111V10, continuous
D111V11, continuous
                 vv
clus              R0 R1 R2 RX
  KLK13 MUTATED    5  0  0  0
  KLK13 WILD-TYPE 74 50  4  3
D111V12, multiclass
    clus
vv   KLK13 MUTATED KLK13 WILD-TYPE
  R0             5              74
  R1             0              50
  R2             0               4
  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"
D111V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLK13 MUTATED       0                         0     5
  KLK13 WILD-TYPE     9                         5   123
D111V14, multiclass
                           clus
vv                          KLK13 MUTATED KLK13 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D111V15, binary
                 cls
clus                0   1
  KLK13 MUTATED     0   4
  KLK13 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK13 MUTATED      0    4
  KLK13 WILD-TYPE    5  101
                        clus
vv                       KLK13 MUTATED KLK13 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             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 68 73
  BRD8 MUTATED BRD8 WILD-TYPE 
             3            141 
  BRD8 MUTATED BRD8 WILD-TYPE 
             3             73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  BRD8 MUTATED BRD8 WILD-TYPE 
         17.03           0.03 
  BRD8 MUTATED BRD8 WILD-TYPE 
         20.19          75.12 
  BRD8 MUTATED BRD8 WILD-TYPE 
         19.82          14.14 
[1] "17.0 - 20.2 (19.8)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "1.5"
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        3        8        23       100         4        4
D112V3, multiclass
           clus
vv          BRD8 MUTATED BRD8 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   122
D112V4, multiclass
       clus
vv      BRD8 MUTATED BRD8 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D112V5, binary
                cls
clus               0   1
  BRD8 MUTATED     0   3
  BRD8 WILD-TYPE  37 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      0    3
  BRD8 WILD-TYPE   37  105
   clus
vv  BRD8 MUTATED BRD8 WILD-TYPE
  0            0             37
  1            3            105
[1] 2 2
[1] FALSE
D112V6, binary
                cls
clus              0  1
  BRD8 MUTATED    1  0
  BRD8 WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      1    0
  BRD8 WILD-TYPE   65    4
   clus
vv  BRD8 MUTATED BRD8 WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D112V7, binary
                cls
clus              0  1
  BRD8 MUTATED    1  2
  BRD8 WILD-TYPE 66 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      1    2
  BRD8 WILD-TYPE   66   77
        clus
vv       BRD8 MUTATED BRD8 WILD-TYPE
  FEMALE            1             66
  MALE              2             77
[1] 2 2
[1] FALSE
D112V8, binary
                cls
clus              0  1
  BRD8 MUTATED    2  0
  BRD8 WILD-TYPE 92 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      2    0
  BRD8 WILD-TYPE   92   36
     clus
vv    BRD8 MUTATED BRD8 WILD-TYPE
  NO             2             92
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BRD8 MUTATED                                     3
  BRD8 WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BRD8 MUTATED                                       0
  BRD8 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BRD8 MUTATED                                                  0
  BRD8 WILD-TYPE                                                2
D112V9, multiclass
                                                  clus
vv                                                 BRD8 MUTATED BRD8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D112V10, continuous
[1] "Remove cluster labels:" "BRD8 MUTATED"          
clus
  BRD8 MUTATED BRD8 WILD-TYPE 
             1             49 
    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-HV-AA8V     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-7887     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
    TCGA-YY-A8LH 
"BRD8 WILD-TYPE" 
D112V11, continuous
[1] "Remove cluster labels:" "BRD8 MUTATED"          
clus
  BRD8 MUTATED BRD8 WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"BRD8 WILD-TYPE" "BRD8 WILD-TYPE" "BRD8 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  BRD8 MUTATED    2  0  0  1
  BRD8 WILD-TYPE 77 50  4  2
D112V12, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  R0            2             77
  R1            0             50
  R2            0              4
  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"
D112V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRD8 MUTATED       0                         1     2
  BRD8 WILD-TYPE     9                         4   126
D112V14, multiclass
                           clus
vv                          BRD8 MUTATED BRD8 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                2            126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V15, binary
                cls
clus               0   1
  BRD8 MUTATED     0   3
  BRD8 WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      0    3
  BRD8 WILD-TYPE    5  102
                        clus
vv                       BRD8 MUTATED BRD8 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(113) Variable = ZMYM2 MUTATION ANALYSIS
D113V1, survival
                 sevent
clus2              0  1
  ZMYM2 MUTATED    0  3
  ZMYM2 WILD-TYPE 68 73
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              3             141 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
           3.95            0.03 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
          19.82           75.12 
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
          10.98           14.40 
[1] "4.0 - 19.8 (11.0)" "0.0 - 75.1 (14.4)"
[1] "hr=" "2.9"
D113V2, 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        3        8        23       100         4        4
D113V3, multiclass
           clus
vv          ZMYM2 MUTATED ZMYM2 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D113V4, multiclass
       clus
vv      ZMYM2 MUTATED ZMYM2 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D113V5, binary
                 cls
clus                0   1
  ZMYM2 MUTATED     0   3
  ZMYM2 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      0    3
  ZMYM2 WILD-TYPE   37  105
   clus
vv  ZMYM2 MUTATED ZMYM2 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D113V6, binary
                 cls
clus               0  1
  ZMYM2 MUTATED    2  0
  ZMYM2 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      2    0
  ZMYM2 WILD-TYPE   64    4
   clus
vv  ZMYM2 MUTATED ZMYM2 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D113V7, binary
                 cls
clus               0  1
  ZMYM2 MUTATED    1  2
  ZMYM2 WILD-TYPE 66 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      1    2
  ZMYM2 WILD-TYPE   66   77
        clus
vv       ZMYM2 MUTATED ZMYM2 WILD-TYPE
  FEMALE             1              66
  MALE               2              77
[1] 2 2
[1] FALSE
D113V8, binary
                 cls
clus               0  1
  ZMYM2 MUTATED    3  0
  ZMYM2 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      3    0
  ZMYM2 WILD-TYPE   91   36
     clus
vv    ZMYM2 MUTATED ZMYM2 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMYM2 MUTATED                                     2
  ZMYM2 WILD-TYPE                                 128
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMYM2 MUTATED                                       1
  ZMYM2 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMYM2 MUTATED                                                  0
  ZMYM2 WILD-TYPE                                                2
D113V9, 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                          128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D113V10, continuous
[1] "Remove cluster labels:" "ZMYM2 MUTATED"         
clus
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
     TCGA-YY-A8LH 
"ZMYM2 WILD-TYPE" 
D113V11, continuous
[1] "Remove cluster labels:" "ZMYM2 MUTATED"         
clus
  ZMYM2 MUTATED ZMYM2 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" "ZMYM2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ZMYM2 MUTATED    2  1  0  0
  ZMYM2 WILD-TYPE 77 49  4  3
D113V12, multiclass
    clus
vv   ZMYM2 MUTATED ZMYM2 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D113V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM2 MUTATED       0                         0     3
  ZMYM2 WILD-TYPE     9                         5   125
D113V14, multiclass
                           clus
vv                          ZMYM2 MUTATED ZMYM2 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V15, binary
                 cls
clus                0   1
  ZMYM2 MUTATED     0   2
  ZMYM2 WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM2 MUTATED      0    2
  ZMYM2 WILD-TYPE    5  103
                        clus
vv                       ZMYM2 MUTATED ZMYM2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(114) Variable = ZNF780A MUTATION ANALYSIS
D114V1, survival
                   sevent
clus2                0  1
  ZNF780A MUTATED    2  3
  ZNF780A WILD-TYPE 66 73
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                5               139 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
                3                73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       19.82        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-A5ST TCGA-IB-A6UF TCGA-IB-A6UG 
       12.00        15.85         7.20        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       22.85        39.98         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ZNF780A MUTATED ZNF780A WILD-TYPE 
             0.23              0.03 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
            16.80             75.12 
  ZNF780A MUTATED ZNF780A WILD-TYPE 
            14.14             14.40 
[1] "0.2 - 16.8 (14.1)" "0.0 - 75.1 (14.4)"
[1] "hr=" "2.2"
D114V2, 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        3        7        23       100         3        4
D114V3, multiclass
           clus
vv          ZNF780A MUTATED ZNF780A WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                1                 7
  STAGE IIA               0                23
  STAGE IIB               3               100
  STAGE III               1                 3
  STAGE IV                0                 4
[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   4  15   121
D114V4, multiclass
       clus
vv      ZNF780A MUTATED ZNF780A WILD-TYPE
  T1                  0                 4
  T2                  1                15
  T3+T4               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"
D114V5, binary
                   cls
clus                  0   1
  ZNF780A MUTATED     1   4
  ZNF780A WILD-TYPE  36 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      1    4
  ZNF780A WILD-TYPE   36  104
   clus
vv  ZNF780A MUTATED ZNF780A WILD-TYPE
  0               1                36
  1               4               104
[1] 2 2
[1] FALSE
D114V6, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    2  0
  ZNF780A WILD-TYPE 64  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      2    0
  ZNF780A WILD-TYPE   64    4
   clus
vv  ZNF780A MUTATED ZNF780A WILD-TYPE
  0               2                64
  1               0                 4
[1] 2 2
[1] FALSE
D114V7, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    3  2
  ZNF780A WILD-TYPE 64 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      3    2
  ZNF780A WILD-TYPE   64   77
        clus
vv       ZNF780A MUTATED ZNF780A WILD-TYPE
  FEMALE               3                64
  MALE                 2                77
[1] 2 2
[1] FALSE
D114V8, binary
                   cls
clus                 0  1
  ZNF780A MUTATED    2  0
  ZNF780A WILD-TYPE 92 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      2    0
  ZNF780A WILD-TYPE   92   36
     clus
vv    ZNF780A MUTATED ZNF780A WILD-TYPE
  NO                2                92
  YES               0                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF780A MUTATED                                     4
  ZNF780A WILD-TYPE                                 126
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF780A MUTATED                                       1
  ZNF780A WILD-TYPE                                    12
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF780A MUTATED                                                  0
  ZNF780A WILD-TYPE                                                2
D114V9, 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                            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           12
  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"
D114V10, continuous
D114V11, continuous
                   vv
clus                R0 R1 R2 RX
  ZNF780A MUTATED    3  2  0  0
  ZNF780A WILD-TYPE 76 48  4  3
D114V12, multiclass
    clus
vv   ZNF780A MUTATED ZNF780A WILD-TYPE
  R0               3                76
  R1               2                48
  R2               0                 4
  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"
D114V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF780A MUTATED       0                         0     5
  ZNF780A WILD-TYPE     9                         5   123
D114V14, multiclass
                           clus
vv                          ZNF780A MUTATED ZNF780A WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   5               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"
D114V15, binary
                   cls
clus                  0   1
  ZNF780A MUTATED     0   5
  ZNF780A WILD-TYPE   5 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF780A MUTATED      0    5
  ZNF780A WILD-TYPE    5  100
                        clus
vv                       ZNF780A MUTATED ZNF780A WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               5               100
[1] 2 2
[1] FALSE

Clustering(115) Variable = MLPH MUTATION ANALYSIS
D115V1, survival
                sevent
clus2             0  1
  MLPH MUTATED    2  1
  MLPH WILD-TYPE 66 75
  MLPH MUTATED MLPH WILD-TYPE 
             3            141 
  MLPH MUTATED MLPH WILD-TYPE 
             1             75 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  MLPH MUTATED MLPH WILD-TYPE 
          7.50           0.03 
  MLPH MUTATED MLPH WILD-TYPE 
         19.82          75.12 
  MLPH MUTATED MLPH WILD-TYPE 
         11.93          14.40 
[1] "7.5 - 19.8 (11.9)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.2"
D115V2, 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        3        8        23       100         4        4
D115V3, multiclass
           clus
vv          MLPH MUTATED MLPH WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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   4  15   123
D115V4, multiclass
       clus
vv      MLPH MUTATED MLPH WILD-TYPE
  T1               0              4
  T2               1             15
  T3+T4            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"
D115V5, binary
                cls
clus               0   1
  MLPH MUTATED     0   3
  MLPH WILD-TYPE  37 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLPH MUTATED      0    3
  MLPH WILD-TYPE   37  105
   clus
vv  MLPH MUTATED MLPH WILD-TYPE
  0            0             37
  1            3            105
[1] 2 2
[1] FALSE
D115V6, binary
                cls
clus              0  1
  MLPH MUTATED    1  0
  MLPH WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLPH MUTATED      1    0
  MLPH WILD-TYPE   65    4
   clus
vv  MLPH MUTATED MLPH WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D115V7, binary
                cls
clus              0  1
  MLPH MUTATED    2  1
  MLPH WILD-TYPE 65 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLPH MUTATED      2    1
  MLPH WILD-TYPE   65   78
        clus
vv       MLPH MUTATED MLPH WILD-TYPE
  FEMALE            2             65
  MALE              1             78
[1] 2 2
[1] FALSE
D115V8, binary
                cls
clus              0  1
  MLPH MUTATED    1  2
  MLPH WILD-TYPE 93 34
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLPH MUTATED      1    2
  MLPH WILD-TYPE   93   34
     clus
vv    MLPH MUTATED MLPH WILD-TYPE
  NO             1             93
  YES            2             34
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MLPH MUTATED                                     3
  MLPH WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MLPH MUTATED                                       0
  MLPH WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MLPH MUTATED                                                  0
  MLPH WILD-TYPE                                                2
D115V9, multiclass
                                                  clus
vv                                                 MLPH MUTATED MLPH WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D115V10, continuous
D115V11, continuous
                vv
clus             R0 R1 R2 RX
  MLPH MUTATED    2  0  0  0
  MLPH WILD-TYPE 77 50  4  3
D115V12, multiclass
[1] "Remove cluster labels:" "MLPH MUTATED"          
clus
  MLPH MUTATED MLPH WILD-TYPE 
             2            134 
    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-HV-A5A6     TCGA-HV-A7OL     TCGA-HV-AA8V 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-HV-AA8X     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-HZ-A9TJ     TCGA-IB-7644     TCGA-IB-7645     TCGA-IB-7646 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-7647     TCGA-IB-7649     TCGA-IB-7652     TCGA-IB-7885 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-7886     TCGA-IB-7887     TCGA-IB-7888     TCGA-IB-7889 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-7890     TCGA-IB-7891     TCGA-IB-7893     TCGA-IB-7897 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SO     TCGA-IB-A5SP 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-A5SQ     TCGA-IB-A5SS     TCGA-IB-A5ST     TCGA-IB-A6UF 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7LX     TCGA-IB-A7M4     TCGA-IB-AAUM 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-AAUN     TCGA-IB-AAUO     TCGA-IB-AAUP     TCGA-IB-AAUQ 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-IB-AAUR     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A8F3     TCGA-LB-A9Q5     TCGA-M8-A5N4 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-OE-A75W     TCGA-Q3-A5QY     TCGA-Q3-AA2A     TCGA-RB-A7B8 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-RB-AA9M     TCGA-S4-A8RM     TCGA-S4-A8RO     TCGA-S4-A8RP 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-US-A774     TCGA-US-A776     TCGA-US-A779     TCGA-US-A77E 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-US-A77G     TCGA-XD-AAUG     TCGA-XD-AAUH     TCGA-XD-AAUI 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-XN-A8T3     TCGA-XN-A8T5     TCGA-YB-A89D 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" "MLPH WILD-TYPE" 
    TCGA-YY-A8LH     TCGA-Z5-AAPL 
"MLPH WILD-TYPE" "MLPH WILD-TYPE" 
D115V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLPH MUTATED       0                         0     3
  MLPH WILD-TYPE     9                         5   125
D115V14, multiclass
                           clus
vv                          MLPH MUTATED MLPH WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V15, binary
                cls
clus               0   1
  MLPH MUTATED     0   3
  MLPH WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLPH MUTATED      0    3
  MLPH WILD-TYPE    5  102
                        clus
vv                       MLPH MUTATED MLPH WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(116) Variable = NLRP6 MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2              0  1
  NLRP6 MUTATED    0  3
  NLRP6 WILD-TYPE 68 73
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             141 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       19.82        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-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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       23.08        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  NLRP6 MUTATED NLRP6 WILD-TYPE 
           4.04            0.03 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          22.85           75.12 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
           8.78           14.40 
[1] "4.0 - 22.9 (8.8)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "2.4"
D116V2, 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        3        8        22       101         4        4
D116V3, multiclass
           clus
vv          NLRP6 MUTATED NLRP6 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             2             101
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D116V4, multiclass
       clus
vv      NLRP6 MUTATED NLRP6 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D116V5, binary
                 cls
clus                0   1
  NLRP6 MUTATED     1   2
  NLRP6 WILD-TYPE  36 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      1    2
  NLRP6 WILD-TYPE   36  106
   clus
vv  NLRP6 MUTATED NLRP6 WILD-TYPE
  0             1              36
  1             2             106
[1] 2 2
[1] FALSE
D116V6, binary
                 cls
clus               0  1
  NLRP6 MUTATED    1  0
  NLRP6 WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      1    0
  NLRP6 WILD-TYPE   65    4
   clus
vv  NLRP6 MUTATED NLRP6 WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D116V7, binary
                 cls
clus               0  1
  NLRP6 MUTATED    1  2
  NLRP6 WILD-TYPE 66 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      1    2
  NLRP6 WILD-TYPE   66   77
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  FEMALE             1              66
  MALE               2              77
[1] 2 2
[1] FALSE
D116V8, binary
                 cls
clus               0  1
  NLRP6 MUTATED    2  1
  NLRP6 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      2    1
  NLRP6 WILD-TYPE   92   35
     clus
vv    NLRP6 MUTATED NLRP6 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NLRP6 MUTATED                                     3
  NLRP6 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NLRP6 MUTATED                                       0
  NLRP6 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NLRP6 MUTATED                                                  0
  NLRP6 WILD-TYPE                                                2
D116V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D116V10, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-S4-A8RM 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
D116V11, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  NLRP6 MUTATED    2  1  0  0
  NLRP6 WILD-TYPE 77 49  4  3
D116V12, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D116V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NLRP6 MUTATED       0                         0     3
  NLRP6 WILD-TYPE     9                         5   125
D116V14, multiclass
                           clus
vv                          NLRP6 MUTATED NLRP6 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V15, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   3
  NLRP6 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    3
  NLRP6 WILD-TYPE    5  102
                        clus
vv                       NLRP6 MUTATED NLRP6 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(117) Variable = SEPT2 MUTATION ANALYSIS
D117V1, survival
                 sevent
clus2              0  1
  SEPT2 MUTATED    0  3
  SEPT2 WILD-TYPE 68 73
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              3             141 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       20.19        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 
       19.82        12.95        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SEPT2 MUTATED SEPT2 WILD-TYPE 
          15.35            0.03 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
          19.82           75.12 
  SEPT2 MUTATED SEPT2 WILD-TYPE 
          17.03           14.14 
[1] "15.3 - 19.8 (17.0)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "1.7"
D117V2, 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        3        8        23       100         4        4
D117V3, multiclass
           clus
vv          SEPT2 MUTATED SEPT2 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D117V4, multiclass
       clus
vv      SEPT2 MUTATED SEPT2 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D117V5, binary
                 cls
clus                0   1
  SEPT2 MUTATED     0   3
  SEPT2 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      0    3
  SEPT2 WILD-TYPE   37  105
   clus
vv  SEPT2 MUTATED SEPT2 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D117V6, binary
                 cls
clus               0  1
  SEPT2 MUTATED    2  0
  SEPT2 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      2    0
  SEPT2 WILD-TYPE   64    4
   clus
vv  SEPT2 MUTATED SEPT2 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D117V7, binary
                 cls
clus               0  1
  SEPT2 MUTATED    2  1
  SEPT2 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      2    1
  SEPT2 WILD-TYPE   65   78
        clus
vv       SEPT2 MUTATED SEPT2 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D117V8, binary
                 cls
clus               0  1
  SEPT2 MUTATED    2  0
  SEPT2 WILD-TYPE 92 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      2    0
  SEPT2 WILD-TYPE   92   36
     clus
vv    SEPT2 MUTATED SEPT2 WILD-TYPE
  NO              2              92
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SEPT2 MUTATED                                     3
  SEPT2 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SEPT2 MUTATED                                       0
  SEPT2 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SEPT2 MUTATED                                                  0
  SEPT2 WILD-TYPE                                                2
D117V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D117V10, continuous
[1] "Remove cluster labels:" "SEPT2 MUTATED"         
clus
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
D117V11, continuous
[1] "Remove cluster labels:" "SEPT2 MUTATED"         
clus
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SEPT2 MUTATED    1  1  0  1
  SEPT2 WILD-TYPE 78 49  4  2
D117V12, multiclass
    clus
vv   SEPT2 MUTATED SEPT2 WILD-TYPE
  R0             1              78
  R1             1              49
  R2             0               4
  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"
D117V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEPT2 MUTATED       0                         1     1
  SEPT2 WILD-TYPE     9                         4   127
D117V14, multiclass
[1] "Remove cluster labels:" "SEPT2 MUTATED"         
clus
  SEPT2 MUTATED SEPT2 WILD-TYPE 
              2             140 
     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-HV-A5A3 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HV-A5A4      TCGA-HV-A5A5      TCGA-HV-A5A6      TCGA-HV-A7OL 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7919      TCGA-HZ-7922 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-7925      TCGA-HZ-8001      TCGA-HZ-8002      TCGA-HZ-8003 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-8005      TCGA-HZ-8315      TCGA-HZ-8317      TCGA-HZ-8519 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-8636      TCGA-HZ-8637      TCGA-HZ-A49G      TCGA-HZ-A49H 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-A49I      TCGA-HZ-A4BH      TCGA-HZ-A4BK      TCGA-HZ-A77O 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-A77P      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-HZ-A9TJ      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-XN-A8T3      TCGA-XN-A8T5 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YH-A8SY      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" "SEPT2 WILD-TYPE" 
D117V15, binary
                 cls
clus                0   1
  SEPT2 MUTATED     0   2
  SEPT2 WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEPT2 MUTATED      0    2
  SEPT2 WILD-TYPE    5  103
                        clus
vv                       SEPT2 MUTATED SEPT2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(118) Variable = MMP13 MUTATION ANALYSIS
D118V1, survival
                 sevent
clus2              0  1
  MMP13 MUTATED    0  3
  MMP13 WILD-TYPE 68 73
  MMP13 MUTATED MMP13 WILD-TYPE 
              3             141 
  MMP13 MUTATED MMP13 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  MMP13 MUTATED MMP13 WILD-TYPE 
           4.04            0.03 
  MMP13 MUTATED MMP13 WILD-TYPE 
          19.82           75.12 
  MMP13 MUTATED MMP13 WILD-TYPE 
           7.36           14.40 
[1] "4.0 - 19.8 (7.4)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "3.2"
D118V2, 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        3        8        23       100         4        4
D118V3, multiclass
           clus
vv          MMP13 MUTATED MMP13 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D118V4, multiclass
       clus
vv      MMP13 MUTATED MMP13 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D118V5, binary
                 cls
clus                0   1
  MMP13 MUTATED     0   3
  MMP13 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    3
  MMP13 WILD-TYPE   37  105
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D118V6, binary
                 cls
clus               0  1
  MMP13 MUTATED    1  0
  MMP13 WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      1    0
  MMP13 WILD-TYPE   65    4
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D118V7, binary
                 cls
clus               0  1
  MMP13 MUTATED    2  1
  MMP13 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      2    1
  MMP13 WILD-TYPE   65   78
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D118V8, binary
                 cls
clus               0  1
  MMP13 MUTATED    3  0
  MMP13 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      3    0
  MMP13 WILD-TYPE   91   36
     clus
vv    MMP13 MUTATED MMP13 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MMP13 MUTATED                                     3
  MMP13 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MMP13 MUTATED                                       0
  MMP13 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MMP13 MUTATED                                                  0
  MMP13 WILD-TYPE                                                2
D118V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D118V10, continuous
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2              48 
     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-HV-AA8V 
"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-7887 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
D118V11, continuous
[1] "Remove cluster labels:" "MMP13 MUTATED"         
clus
  MMP13 MUTATED MMP13 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"MMP13 WILD-TYPE" "MMP13 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  MMP13 MUTATED    2  1  0  0
  MMP13 WILD-TYPE 77 49  4  3
D118V12, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D118V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP13 MUTATED       0                         0     3
  MMP13 WILD-TYPE     9                         5   125
D118V14, multiclass
                           clus
vv                          MMP13 MUTATED MMP13 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V15, binary
                 cls
clus                0   1
  MMP13 MUTATED     0   3
  MMP13 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED      0    3
  MMP13 WILD-TYPE    5  102
                        clus
vv                       MMP13 MUTATED MMP13 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(119) Variable = OXR1 MUTATION ANALYSIS
D119V1, survival
                sevent
clus2             0  1
  OXR1 MUTATED    0  3
  OXR1 WILD-TYPE 68 73
  OXR1 MUTATED OXR1 WILD-TYPE 
             3            141 
  OXR1 MUTATED OXR1 WILD-TYPE 
             3             73 
$`OXR1 MUTATED`
TCGA-3A-A9IZ TCGA-HZ-7925 TCGA-IB-7649 
       10.13        20.19        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       33.57        15.06        34.09        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  OXR1 MUTATED OXR1 WILD-TYPE 
         10.13           0.03 
  OXR1 MUTATED OXR1 WILD-TYPE 
         20.19          75.12 
  OXR1 MUTATED OXR1 WILD-TYPE 
         15.35          14.17 
[1] "10.1 - 20.2 (15.3)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "2.1"
D119V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OXR1 MUTATED          0        0         0         3         0        0
  OXR1 WILD-TYPE        3        8        23       100         4        4
D119V3, multiclass
           clus
vv          OXR1 MUTATED OXR1 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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     3
  OXR1 WILD-TYPE   4  16   122
D119V4, multiclass
       clus
vv      OXR1 MUTATED OXR1 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D119V5, binary
                cls
clus               0   1
  OXR1 MUTATED     0   3
  OXR1 WILD-TYPE  37 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      0    3
  OXR1 WILD-TYPE   37  105
   clus
vv  OXR1 MUTATED OXR1 WILD-TYPE
  0            0             37
  1            3            105
[1] 2 2
[1] FALSE
D119V6, binary
                cls
clus              0  1
  OXR1 MUTATED    1  0
  OXR1 WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      1    0
  OXR1 WILD-TYPE   65    4
   clus
vv  OXR1 MUTATED OXR1 WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D119V7, binary
                cls
clus              0  1
  OXR1 MUTATED    1  2
  OXR1 WILD-TYPE 66 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      1    2
  OXR1 WILD-TYPE   66   77
        clus
vv       OXR1 MUTATED OXR1 WILD-TYPE
  FEMALE            1             66
  MALE              2             77
[1] 2 2
[1] FALSE
D119V8, binary
                cls
clus              0  1
  OXR1 MUTATED    3  0
  OXR1 WILD-TYPE 91 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      3    0
  OXR1 WILD-TYPE   91   36
     clus
vv    OXR1 MUTATED OXR1 WILD-TYPE
  NO             3             91
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OXR1 MUTATED                                     3
  OXR1 WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OXR1 MUTATED                                       0
  OXR1 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OXR1 MUTATED                                                  0
  OXR1 WILD-TYPE                                                2
D119V9, multiclass
                                                  clus
vv                                                 OXR1 MUTATED OXR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D119V10, continuous
[1] "Remove cluster labels:" "OXR1 MUTATED"          
clus
  OXR1 MUTATED OXR1 WILD-TYPE 
             1             49 
    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-HV-AA8V     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-7887     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-YY-A8LH 
"OXR1 WILD-TYPE" 
D119V11, continuous
[1] "Remove cluster labels:" "OXR1 MUTATED"          
clus
  OXR1 MUTATED OXR1 WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  OXR1 MUTATED    1  2  0  0
  OXR1 WILD-TYPE 78 48  4  3
D119V12, multiclass
    clus
vv   OXR1 MUTATED OXR1 WILD-TYPE
  R0            1             78
  R1            2             48
  R2            0              4
  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"
D119V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OXR1 MUTATED       0                         0     2
  OXR1 WILD-TYPE     9                         5   126
D119V14, multiclass
[1] "Remove cluster labels:" "OXR1 MUTATED"          
clus
  OXR1 MUTATED OXR1 WILD-TYPE 
             2            140 
    TCGA-2J-AAB1     TCGA-2J-AAB4     TCGA-2J-AAB6     TCGA-2J-AAB8 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-2J-AAB9     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-2J-AABH     TCGA-2J-AABK     TCGA-2J-AABO     TCGA-2J-AABR 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-2J-AABU     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-2L-AAQI     TCGA-2L-AAQJ     TCGA-2L-AAQL     TCGA-3A-A9I5 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-3A-A9I7     TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IC 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-3A-A9IH     TCGA-3A-A9IU     TCGA-3A-A9IX     TCGA-3A-A9J0 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-3E-AAAY     TCGA-3E-AAAZ     TCGA-F2-6879     TCGA-F2-A44G 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-F2-A44H     TCGA-F2-A7TX     TCGA-F2-A8YN     TCGA-FB-A4P5 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-FB-A4P6     TCGA-FB-A545     TCGA-FB-A5VM     TCGA-FB-A78T 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPU     TCGA-FB-AAPY     TCGA-FB-AAPZ 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-FB-AAQ0     TCGA-FB-AAQ1     TCGA-FB-AAQ2     TCGA-FB-AAQ3 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-H6-8124     TCGA-H6-A45N     TCGA-HV-A5A3     TCGA-HV-A5A4 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-HV-A5A5     TCGA-HV-A5A6     TCGA-HV-A7OL     TCGA-HV-AA8V 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-HV-AA8X     TCGA-HZ-7919     TCGA-HZ-7922     TCGA-HZ-7926 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-HZ-8001     TCGA-HZ-8002     TCGA-HZ-8003     TCGA-HZ-8005 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-HZ-8315     TCGA-HZ-8317     TCGA-HZ-8519     TCGA-HZ-8636 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-HZ-8637     TCGA-HZ-A49G     TCGA-HZ-A49H     TCGA-HZ-A49I 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-HZ-A4BH     TCGA-HZ-A4BK     TCGA-HZ-A77O     TCGA-HZ-A77P 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-HZ-A9TJ 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7646     TCGA-IB-7647     TCGA-IB-7651 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-7652     TCGA-IB-7885     TCGA-IB-7886     TCGA-IB-7887 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-7888     TCGA-IB-7889     TCGA-IB-7891     TCGA-IB-7893 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-7897     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SO 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-A5SP     TCGA-IB-A5SQ     TCGA-IB-A5SS     TCGA-IB-A5ST 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7LX     TCGA-IB-A7M4 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-AAUM     TCGA-IB-AAUN     TCGA-IB-AAUO     TCGA-IB-AAUP 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUR     TCGA-IB-AAUS     TCGA-IB-AAUT 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-IB-AAUU     TCGA-LB-A7SX     TCGA-LB-A8F3     TCGA-LB-A9Q5 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-PZ-A5RE     TCGA-Q3-A5QY     TCGA-Q3-AA2A 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-RB-A7B8     TCGA-RB-AA9M     TCGA-S4-A8RM     TCGA-S4-A8RO 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-US-A776     TCGA-US-A779 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-US-A77E     TCGA-US-A77G     TCGA-XD-AAUG     TCGA-XD-AAUH 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-XD-AAUI     TCGA-XD-AAUL     TCGA-XN-A8T3     TCGA-XN-A8T5 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
    TCGA-YB-A89D     TCGA-YH-A8SY     TCGA-YY-A8LH     TCGA-Z5-AAPL 
"OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" "OXR1 WILD-TYPE" 
D119V15, binary
                cls
clus               0   1
  OXR1 MUTATED     1   1
  OXR1 WILD-TYPE   4 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXR1 MUTATED      1    1
  OXR1 WILD-TYPE    4  104
                        clus
vv                       OXR1 MUTATED OXR1 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            1            104
[1] 2 2
[1] FALSE

Clustering(120) Variable = LACTB MUTATION ANALYSIS
D120V1, survival
                 sevent
clus2              0  1
  LACTB MUTATED    1  2
  LACTB WILD-TYPE 67 74
  LACTB MUTATED LACTB WILD-TYPE 
              3             141 
  LACTB MUTATED LACTB WILD-TYPE 
              2              74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  LACTB MUTATED LACTB WILD-TYPE 
          15.35            0.03 
  LACTB MUTATED LACTB WILD-TYPE 
          41.33           75.12 
  LACTB MUTATED LACTB WILD-TYPE 
          19.82           14.14 
[1] "15.3 - 41.3 (19.8)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "1.2"
D120V2, 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        3        8        23       100         4        4
D120V3, multiclass
           clus
vv          LACTB MUTATED LACTB WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D120V4, multiclass
       clus
vv      LACTB MUTATED LACTB WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D120V5, binary
                 cls
clus                0   1
  LACTB MUTATED     0   3
  LACTB WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      0    3
  LACTB WILD-TYPE   37  105
   clus
vv  LACTB MUTATED LACTB WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D120V6, binary
                 cls
clus               0  1
  LACTB MUTATED    3  0
  LACTB WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      3    0
  LACTB WILD-TYPE   63    4
   clus
vv  LACTB MUTATED LACTB WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D120V7, binary
                 cls
clus               0  1
  LACTB MUTATED    3  0
  LACTB WILD-TYPE 64 79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      3    0
  LACTB WILD-TYPE   64   79
        clus
vv       LACTB MUTATED LACTB WILD-TYPE
  FEMALE             3              64
  MALE               0              79
[1] 2 2
[1] FALSE
D120V8, binary
                 cls
clus               0  1
  LACTB MUTATED    3  0
  LACTB WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      3    0
  LACTB WILD-TYPE   91   36
     clus
vv    LACTB MUTATED LACTB WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LACTB MUTATED                                     3
  LACTB WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LACTB MUTATED                                       0
  LACTB WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LACTB MUTATED                                                  0
  LACTB WILD-TYPE                                                2
D120V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D120V10, continuous
D120V11, continuous
                 vv
clus              R0 R1 R2 RX
  LACTB MUTATED    2  1  0  0
  LACTB WILD-TYPE 77 49  4  3
D120V12, multiclass
    clus
vv   LACTB MUTATED LACTB WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D120V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LACTB MUTATED       0                         0     2
  LACTB WILD-TYPE     9                         5   126
D120V14, multiclass
[1] "Remove cluster labels:" "LACTB MUTATED"         
clus
  LACTB MUTATED LACTB WILD-TYPE 
              2             140 
     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-HV-A5A3 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HV-A5A4      TCGA-HV-A5A5      TCGA-HV-A5A6      TCGA-HV-A7OL 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HV-AA8X      TCGA-HZ-7919      TCGA-HZ-7922 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-7925      TCGA-HZ-7926      TCGA-HZ-8001      TCGA-HZ-8002 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-8003      TCGA-HZ-8005      TCGA-HZ-8315      TCGA-HZ-8317 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-8519      TCGA-HZ-8636      TCGA-HZ-8637      TCGA-HZ-A49G 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-A49H      TCGA-HZ-A49I      TCGA-HZ-A4BH      TCGA-HZ-A4BK 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-A77O      TCGA-HZ-A77P      TCGA-HZ-A77Q      TCGA-HZ-A8P0 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-HZ-A8P1      TCGA-HZ-A9TJ      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-XN-A8T3      TCGA-XN-A8T5 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YH-A8SY      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" "LACTB WILD-TYPE" 
D120V15, binary
                 cls
clus                0   1
  LACTB MUTATED     0   2
  LACTB WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LACTB MUTATED      0    2
  LACTB WILD-TYPE    5  103
                        clus
vv                       LACTB MUTATED LACTB WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(121) Variable = SYCP2 MUTATION ANALYSIS
D121V1, survival
                 sevent
clus2              0  1
  SYCP2 MUTATED    2  3
  SYCP2 WILD-TYPE 66 73
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              5             139 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-AAUU TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SYCP2 MUTATED SYCP2 WILD-TYPE 
           3.12            0.03 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
          41.33           75.12 
  SYCP2 MUTATED SYCP2 WILD-TYPE 
          19.82           14.17 
[1] "3.1 - 41.3 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1"  
D121V2, 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        3        8        23        98         4        4
D121V3, multiclass
           clus
vv          SYCP2 MUTATED SYCP2 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              0               4
[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   4  15   121
D121V4, multiclass
       clus
vv      SYCP2 MUTATED SYCP2 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D121V5, binary
                 cls
clus                0   1
  SYCP2 MUTATED     0   5
  SYCP2 WILD-TYPE  37 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      0    5
  SYCP2 WILD-TYPE   37  103
   clus
vv  SYCP2 MUTATED SYCP2 WILD-TYPE
  0             0              37
  1             5             103
[1] 2 2
[1] FALSE
D121V6, binary
                 cls
clus               0  1
  SYCP2 MUTATED    4  0
  SYCP2 WILD-TYPE 62  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      4    0
  SYCP2 WILD-TYPE   62    4
   clus
vv  SYCP2 MUTATED SYCP2 WILD-TYPE
  0             4              62
  1             0               4
[1] 2 2
[1] FALSE
D121V7, binary
                 cls
clus               0  1
  SYCP2 MUTATED    2  3
  SYCP2 WILD-TYPE 65 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      2    3
  SYCP2 WILD-TYPE   65   76
        clus
vv       SYCP2 MUTATED SYCP2 WILD-TYPE
  FEMALE             2              65
  MALE               3              76
[1] 2 2
[1] FALSE
D121V8, binary
                 cls
clus               0  1
  SYCP2 MUTATED    5  0
  SYCP2 WILD-TYPE 89 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      5    0
  SYCP2 WILD-TYPE   89   36
     clus
vv    SYCP2 MUTATED SYCP2 WILD-TYPE
  NO              5              89
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYCP2 MUTATED                                     4
  SYCP2 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYCP2 MUTATED                                       0
  SYCP2 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYCP2 MUTATED                                                  1
  SYCP2 WILD-TYPE                                                1
D121V9, 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                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D121V10, continuous
D121V11, continuous
                 vv
clus              R0 R1 R2 RX
  SYCP2 MUTATED    3  2  0  0
  SYCP2 WILD-TYPE 76 48  4  3
D121V12, multiclass
    clus
vv   SYCP2 MUTATED SYCP2 WILD-TYPE
  R0             3              76
  R1             2              48
  R2             0               4
  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"
D121V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYCP2 MUTATED       0                         0     5
  SYCP2 WILD-TYPE     9                         5   123
D121V14, multiclass
                           clus
vv                          SYCP2 MUTATED SYCP2 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D121V15, binary
                 cls
clus                0   1
  SYCP2 MUTATED     0   4
  SYCP2 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYCP2 MUTATED      0    4
  SYCP2 WILD-TYPE    5  101
                        clus
vv                       SYCP2 MUTATED SYCP2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(122) Variable = WDHD1 MUTATION ANALYSIS
D122V1, survival
                 sevent
clus2              0  1
  WDHD1 MUTATED    0  3
  WDHD1 WILD-TYPE 68 73
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              3             141 
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
       20.19        17.03        23.21        12.03        19.59         9.83 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
       12.43        14.93        17.92        21.70        16.14         6.38 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  WDHD1 MUTATED WDHD1 WILD-TYPE 
           3.95            0.03 
  WDHD1 MUTATED WDHD1 WILD-TYPE 
          19.82           75.12 
  WDHD1 MUTATED WDHD1 WILD-TYPE 
          10.13           14.40 
[1] "4.0 - 19.8 (10.1)" "0.0 - 75.1 (14.4)"
[1] "hr=" "3"  
D122V2, 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        3        8        23       100         4        4
D122V3, multiclass
           clus
vv          WDHD1 MUTATED WDHD1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D122V4, multiclass
       clus
vv      WDHD1 MUTATED WDHD1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D122V5, binary
                 cls
clus                0   1
  WDHD1 MUTATED     0   3
  WDHD1 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDHD1 MUTATED      0    3
  WDHD1 WILD-TYPE   37  105
   clus
vv  WDHD1 MUTATED WDHD1 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D122V6, binary
                 cls
clus               0  1
  WDHD1 MUTATED    1  0
  WDHD1 WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDHD1 MUTATED      1    0
  WDHD1 WILD-TYPE   65    4
   clus
vv  WDHD1 MUTATED WDHD1 WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D122V7, binary
                 cls
clus               0  1
  WDHD1 MUTATED    1  2
  WDHD1 WILD-TYPE 66 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDHD1 MUTATED      1    2
  WDHD1 WILD-TYPE   66   77
        clus
vv       WDHD1 MUTATED WDHD1 WILD-TYPE
  FEMALE             1              66
  MALE               2              77
[1] 2 2
[1] FALSE
D122V8, binary
                 cls
clus               0  1
  WDHD1 MUTATED    2  1
  WDHD1 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDHD1 MUTATED      2    1
  WDHD1 WILD-TYPE   92   35
     clus
vv    WDHD1 MUTATED WDHD1 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WDHD1 MUTATED                                     3
  WDHD1 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WDHD1 MUTATED                                       0
  WDHD1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WDHD1 MUTATED                                                  0
  WDHD1 WILD-TYPE                                                2
D122V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D122V10, continuous
[1] "Remove cluster labels:" "WDHD1 MUTATED"         
clus
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
     TCGA-YY-A8LH 
"WDHD1 WILD-TYPE" 
D122V11, continuous
[1] "Remove cluster labels:" "WDHD1 MUTATED"         
clus
  WDHD1 MUTATED WDHD1 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" "WDHD1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  WDHD1 MUTATED    1  2  0  0
  WDHD1 WILD-TYPE 78 48  4  3
D122V12, multiclass
    clus
vv   WDHD1 MUTATED WDHD1 WILD-TYPE
  R0             1              78
  R1             2              48
  R2             0               4
  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"
D122V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDHD1 MUTATED       0                         0     3
  WDHD1 WILD-TYPE     9                         5   125
D122V14, multiclass
                           clus
vv                          WDHD1 MUTATED WDHD1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V15, binary
                 cls
clus                0   1
  WDHD1 MUTATED     0   3
  WDHD1 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDHD1 MUTATED      0    3
  WDHD1 WILD-TYPE    5  102
                        clus
vv                       WDHD1 MUTATED WDHD1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(123) Variable = RTTN MUTATION ANALYSIS
D123V1, survival
                sevent
clus2             0  1
  RTTN MUTATED    1  4
  RTTN WILD-TYPE 67 72
  RTTN MUTATED RTTN WILD-TYPE 
             5            139 
  RTTN MUTATED RTTN WILD-TYPE 
             4             72 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03        19.59         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-HZ-A9TJ 
        6.38        21.60         5.26        10.85         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       22.85        39.98         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  RTTN MUTATED RTTN WILD-TYPE 
          1.08           0.03 
  RTTN MUTATED RTTN WILD-TYPE 
         20.19          75.12 
  RTTN MUTATED RTTN WILD-TYPE 
         16.80          14.17 
[1] "1.1 - 20.2 (16.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.7"
D123V2, 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        3        8        23        98         4        4
D123V3, multiclass
           clus
vv          RTTN MUTATED RTTN WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            5             98
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   120
D123V4, multiclass
       clus
vv      RTTN MUTATED RTTN WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D123V5, binary
                cls
clus               0   1
  RTTN MUTATED     0   5
  RTTN WILD-TYPE  37 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      0    5
  RTTN WILD-TYPE   37  103
   clus
vv  RTTN MUTATED RTTN WILD-TYPE
  0            0             37
  1            5            103
[1] 2 2
[1] FALSE
D123V6, binary
                cls
clus              0  1
  RTTN MUTATED    1  0
  RTTN WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      1    0
  RTTN WILD-TYPE   65    4
   clus
vv  RTTN MUTATED RTTN WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D123V7, binary
                cls
clus              0  1
  RTTN MUTATED    3  2
  RTTN WILD-TYPE 64 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      3    2
  RTTN WILD-TYPE   64   77
        clus
vv       RTTN MUTATED RTTN WILD-TYPE
  FEMALE            3             64
  MALE              2             77
[1] 2 2
[1] FALSE
D123V8, binary
                cls
clus              0  1
  RTTN MUTATED    3  0
  RTTN WILD-TYPE 91 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      3    0
  RTTN WILD-TYPE   91   36
     clus
vv    RTTN MUTATED RTTN WILD-TYPE
  NO             3             91
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RTTN MUTATED                                     3
  RTTN WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RTTN MUTATED                                       2
  RTTN WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RTTN MUTATED                                                  0
  RTTN WILD-TYPE                                                2
D123V9, multiclass
                                                  clus
vv                                                 RTTN MUTATED RTTN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             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"
D123V10, continuous
[1] "Remove cluster labels:" "RTTN MUTATED"          
clus
  RTTN MUTATED RTTN WILD-TYPE 
             2             48 
    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-HV-AA8V     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-7887 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" "RTTN WILD-TYPE" 
D123V11, continuous
[1] "Remove cluster labels:" "RTTN MUTATED"          
clus
  RTTN MUTATED RTTN WILD-TYPE 
             2             38 
    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-XN-A8T5     TCGA-YY-A8LH 
"RTTN WILD-TYPE" "RTTN WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  RTTN MUTATED    4  1  0  0
  RTTN WILD-TYPE 75 49  4  3
D123V12, multiclass
    clus
vv   RTTN MUTATED RTTN WILD-TYPE
  R0            4             75
  R1            1             49
  R2            0              4
  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"
D123V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RTTN MUTATED       0                         0     5
  RTTN WILD-TYPE     9                         5   123
D123V14, multiclass
                           clus
vv                          RTTN MUTATED RTTN WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            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"
D123V15, binary
                cls
clus               0   1
  RTTN MUTATED     0   5
  RTTN WILD-TYPE   5 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTTN MUTATED      0    5
  RTTN WILD-TYPE    5  100
                        clus
vv                       RTTN MUTATED RTTN WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5            100
[1] 2 2
[1] FALSE

Clustering(124) Variable = TDRD5 MUTATION ANALYSIS
D124V1, survival
                 sevent
clus2              0  1
  TDRD5 MUTATED    0  4
  TDRD5 WILD-TYPE 68 72
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              4             140 
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              4              72 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       20.19        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       19.82        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-AAUP TCGA-IB-AAUQ 
        8.22        15.88         0.26         4.73        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  TDRD5 MUTATED TDRD5 WILD-TYPE 
           7.86            0.03 
  TDRD5 MUTATED TDRD5 WILD-TYPE 
          19.82           75.12 
  TDRD5 MUTATED TDRD5 WILD-TYPE 
         14.990          14.285 
[1] "7.9 - 19.8 (15.0)" "0.0 - 75.1 (14.3)"
[1] "hr=" "2.2"
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        3        8        23       100         4        3
D124V3, multiclass
           clus
vv          TDRD5 MUTATED TDRD5 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              1               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
  TDRD5 MUTATED     0   0     4
  TDRD5 WILD-TYPE   4  16   121
D124V4, multiclass
       clus
vv      TDRD5 MUTATED TDRD5 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D124V5, binary
                 cls
clus                0   1
  TDRD5 MUTATED     0   4
  TDRD5 WILD-TYPE  37 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD5 MUTATED      0    4
  TDRD5 WILD-TYPE   37  104
   clus
vv  TDRD5 MUTATED TDRD5 WILD-TYPE
  0             0              37
  1             4             104
[1] 2 2
[1] FALSE
D124V6, binary
                 cls
clus               0  1
  TDRD5 MUTATED    2  1
  TDRD5 WILD-TYPE 64  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD5 MUTATED      2    1
  TDRD5 WILD-TYPE   64    3
   clus
vv  TDRD5 MUTATED TDRD5 WILD-TYPE
  0             2              64
  1             1               3
[1] 2 2
[1] FALSE
D124V7, binary
                 cls
clus               0  1
  TDRD5 MUTATED    3  1
  TDRD5 WILD-TYPE 64 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD5 MUTATED      3    1
  TDRD5 WILD-TYPE   64   78
        clus
vv       TDRD5 MUTATED TDRD5 WILD-TYPE
  FEMALE             3              64
  MALE               1              78
[1] 2 2
[1] FALSE
D124V8, binary
                 cls
clus               0  1
  TDRD5 MUTATED    3  0
  TDRD5 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD5 MUTATED      3    0
  TDRD5 WILD-TYPE   91   36
     clus
vv    TDRD5 MUTATED TDRD5 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TDRD5 MUTATED                                     4
  TDRD5 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TDRD5 MUTATED                                       0
  TDRD5 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TDRD5 MUTATED                                                  0
  TDRD5 WILD-TYPE                                                2
D124V9, 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                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D124V10, continuous
[1] "Remove cluster labels:" "TDRD5 MUTATED"         
clus
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
D124V11, continuous
[1] "Remove cluster labels:" "TDRD5 MUTATED"         
clus
  TDRD5 MUTATED TDRD5 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"TDRD5 WILD-TYPE" "TDRD5 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  TDRD5 MUTATED    1  2  0  1
  TDRD5 WILD-TYPE 78 48  4  2
D124V12, multiclass
    clus
vv   TDRD5 MUTATED TDRD5 WILD-TYPE
  R0             1              78
  R1             2              48
  R2             0               4
  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"
D124V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TDRD5 MUTATED       0                         1     3
  TDRD5 WILD-TYPE     9                         4   125
D124V14, multiclass
                           clus
vv                          TDRD5 MUTATED TDRD5 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V15, binary
                 cls
clus                0   1
  TDRD5 MUTATED     0   4
  TDRD5 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD5 MUTATED      0    4
  TDRD5 WILD-TYPE    5  101
                        clus
vv                       TDRD5 MUTATED TDRD5 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(125) Variable = SEPHS2 MUTATION ANALYSIS
D125V1, survival
                  sevent
clus2               0  1
  SEPHS2 MUTATED    2  3
  SEPHS2 WILD-TYPE 66 73
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               5              139 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
               3               73 
$`SEPHS2 MUTATED`
TCGA-3A-A9IX TCGA-F2-A8YN TCGA-FB-A5VM TCGA-IB-A5SS TCGA-RB-A7B8 
       34.09        17.00        16.37        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       33.57        15.06        10.13        24.43        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 
       12.66         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-A5ST TCGA-IB-A6UF TCGA-IB-A6UG TCGA-IB-A7LX 
       15.85         7.20        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
           15.12             0.03 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
           34.09            75.12 
  SEPHS2 MUTATED SEPHS2 WILD-TYPE 
           16.37            13.84 
[1] "15.1 - 34.1 (16.4)" "0.0 - 75.1 (13.8)" 
[1] "hr=" "1"  
D125V2, 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        2        7        22       101         4        4
D125V3, multiclass
           clus
vv          SEPHS2 MUTATED SEPHS2 WILD-TYPE
  STAGE IA               1                2
  STAGE IB               1                7
  STAGE IIA              1               22
  STAGE IIB              2              101
  STAGE III              0                4
  STAGE IV               0                4
[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   3  15   122
D125V4, multiclass
       clus
vv      SEPHS2 MUTATED SEPHS2 WILD-TYPE
  T1                 1                3
  T2                 1               15
  T3+T4              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"
D125V5, binary
                  cls
clus                 0   1
  SEPHS2 MUTATED     3   2
  SEPHS2 WILD-TYPE  34 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      3    2
  SEPHS2 WILD-TYPE   34  106
   clus
vv  SEPHS2 MUTATED SEPHS2 WILD-TYPE
  0              3               34
  1              2              106
[1] 2 2
[1] FALSE
D125V6, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    3  0
  SEPHS2 WILD-TYPE 63  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      3    0
  SEPHS2 WILD-TYPE   63    4
   clus
vv  SEPHS2 MUTATED SEPHS2 WILD-TYPE
  0              3               63
  1              0                4
[1] 2 2
[1] FALSE
D125V7, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    2  3
  SEPHS2 WILD-TYPE 65 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      2    3
  SEPHS2 WILD-TYPE   65   76
        clus
vv       SEPHS2 MUTATED SEPHS2 WILD-TYPE
  FEMALE              2               65
  MALE                3               76
[1] 2 2
[1] FALSE
D125V8, binary
                  cls
clus                0  1
  SEPHS2 MUTATED    4  1
  SEPHS2 WILD-TYPE 90 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      4    1
  SEPHS2 WILD-TYPE   90   35
     clus
vv    SEPHS2 MUTATED SEPHS2 WILD-TYPE
  NO               4               90
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SEPHS2 MUTATED                                     4
  SEPHS2 WILD-TYPE                                 126
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SEPHS2 MUTATED                                       1
  SEPHS2 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SEPHS2 MUTATED                                                  0
  SEPHS2 WILD-TYPE                                                2
D125V9, 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                           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D125V10, continuous
D125V11, continuous
                  vv
clus               R0 R1 R2 RX
  SEPHS2 MUTATED    4  1  0  0
  SEPHS2 WILD-TYPE 75 49  4  3
D125V12, multiclass
    clus
vv   SEPHS2 MUTATED SEPHS2 WILD-TYPE
  R0              4               75
  R1              1               49
  R2              0                4
  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"
D125V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEPHS2 MUTATED       0                         0     5
  SEPHS2 WILD-TYPE     9                         5   123
D125V14, multiclass
                           clus
vv                          SEPHS2 MUTATED SEPHS2 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              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"
D125V15, binary
                  cls
clus                 0   1
  SEPHS2 MUTATED     0   5
  SEPHS2 WILD-TYPE   5 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEPHS2 MUTATED      0    5
  SEPHS2 WILD-TYPE    5  100
                        clus
vv                       SEPHS2 MUTATED SEPHS2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5              100
[1] 2 2
[1] FALSE

Clustering(126) Variable = ACTRT2 MUTATION ANALYSIS
D126V1, survival
                  sevent
clus2               0  1
  ACTRT2 MUTATED    1  2
  ACTRT2 WILD-TYPE 67 74
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               3              141 
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               2               74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03        19.59         3.95         9.83 
TCGA-HZ-8317 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH 
       12.43        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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
            4.04             0.03 
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
           20.19            75.12 
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
           14.93            14.17 
[1] "4.0 - 20.2 (14.9)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.6"
D126V2, 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        2        8        23       101         4        4
D126V3, multiclass
           clus
vv          ACTRT2 MUTATED ACTRT2 WILD-TYPE
  STAGE IA               1                2
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              2              101
  STAGE III              0                4
  STAGE IV               0                4
[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   3  16   123
D126V4, multiclass
       clus
vv      ACTRT2 MUTATED ACTRT2 WILD-TYPE
  T1                 1                3
  T2                 0               16
  T3+T4              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"
D126V5, binary
                  cls
clus                 0   1
  ACTRT2 MUTATED     1   2
  ACTRT2 WILD-TYPE  36 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT2 MUTATED      1    2
  ACTRT2 WILD-TYPE   36  106
   clus
vv  ACTRT2 MUTATED ACTRT2 WILD-TYPE
  0              1               36
  1              2              106
[1] 2 2
[1] FALSE
D126V6, binary
                  cls
clus                0  1
  ACTRT2 MUTATED    1  0
  ACTRT2 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT2 MUTATED      1    0
  ACTRT2 WILD-TYPE   65    4
   clus
vv  ACTRT2 MUTATED ACTRT2 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D126V7, binary
                  cls
clus                0  1
  ACTRT2 MUTATED    0  3
  ACTRT2 WILD-TYPE 67 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT2 MUTATED      0    3
  ACTRT2 WILD-TYPE   67   76
        clus
vv       ACTRT2 MUTATED ACTRT2 WILD-TYPE
  FEMALE              0               67
  MALE                3               76
[1] 2 2
[1] FALSE
D126V8, binary
                  cls
clus                0  1
  ACTRT2 MUTATED    2  1
  ACTRT2 WILD-TYPE 92 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT2 MUTATED      2    1
  ACTRT2 WILD-TYPE   92   35
     clus
vv    ACTRT2 MUTATED ACTRT2 WILD-TYPE
  NO               2               92
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ACTRT2 MUTATED                                     2
  ACTRT2 WILD-TYPE                                 128
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ACTRT2 MUTATED                                       1
  ACTRT2 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ACTRT2 MUTATED                                                  0
  ACTRT2 WILD-TYPE                                                2
D126V9, 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                           128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D126V10, continuous
[1] "Remove cluster labels:" "ACTRT2 MUTATED"        
clus
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               1               49 
      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-HV-AA8V       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-7887       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-A5SS       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-S4-A8RP       TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
      TCGA-YY-A8LH 
"ACTRT2 WILD-TYPE" 
D126V11, continuous
[1] "Remove cluster labels:" "ACTRT2 MUTATED"        
clus
  ACTRT2 MUTATED ACTRT2 WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" "ACTRT2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ACTRT2 MUTATED    2  1  0  0
  ACTRT2 WILD-TYPE 77 49  4  3
D126V12, multiclass
    clus
vv   ACTRT2 MUTATED ACTRT2 WILD-TYPE
  R0              2               77
  R1              1               49
  R2              0                4
  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"
D126V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACTRT2 MUTATED       0                         0     3
  ACTRT2 WILD-TYPE     9                         5   125
D126V14, multiclass
                           clus
vv                          ACTRT2 MUTATED ACTRT2 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V15, binary
                  cls
clus                 0   1
  ACTRT2 MUTATED     0   3
  ACTRT2 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT2 MUTATED      0    3
  ACTRT2 WILD-TYPE    5  102
                        clus
vv                       ACTRT2 MUTATED ACTRT2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(127) Variable = DNAH7 MUTATION ANALYSIS
D127V1, survival
                 sevent
clus2              0  1
  DNAH7 MUTATED    4  3
  DNAH7 WILD-TYPE 64 73
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              7             137 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
       21.60         5.26        10.85         0.23        19.82        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-Q3-A5QY TCGA-Q3-AA2A TCGA-RB-A7B8 TCGA-S4-A8RM 
       19.20         8.78        13.68         3.12        15.32        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
        0.39        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       23.67        11.51        12.76        66.28        15.35 

  DNAH7 MUTATED DNAH7 WILD-TYPE 
           1.08            0.03 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
          41.33           75.12 
  DNAH7 MUTATED DNAH7 WILD-TYPE 
          19.82           14.14 
[1] "1.1 - 41.3 (19.8)" "0.0 - 75.1 (14.1)"
[1] "hr=" "1.5"
D127V2, 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        3        8        23        96         4        4
D127V3, multiclass
           clus
vv          DNAH7 MUTATED DNAH7 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             7              96
  STAGE III             0               4
  STAGE IV              0               4
[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   3  15   120
D127V4, multiclass
       clus
vv      DNAH7 MUTATED DNAH7 WILD-TYPE
  T1                1               3
  T2                1              15
  T3+T4             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"
D127V5, binary
                 cls
clus                0   1
  DNAH7 MUTATED     0   7
  DNAH7 WILD-TYPE  37 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      0    7
  DNAH7 WILD-TYPE   37  101
   clus
vv  DNAH7 MUTATED DNAH7 WILD-TYPE
  0             0              37
  1             7             101
[1] 2 2
[1] FALSE
D127V6, binary
                 cls
clus               0  1
  DNAH7 MUTATED    2  0
  DNAH7 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      2    0
  DNAH7 WILD-TYPE   64    4
   clus
vv  DNAH7 MUTATED DNAH7 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D127V7, binary
                 cls
clus               0  1
  DNAH7 MUTATED    4  3
  DNAH7 WILD-TYPE 63 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      4    3
  DNAH7 WILD-TYPE   63   76
        clus
vv       DNAH7 MUTATED DNAH7 WILD-TYPE
  FEMALE             4              63
  MALE               3              76
[1] 2 2
[1] FALSE
D127V8, binary
                 cls
clus               0  1
  DNAH7 MUTATED    4  2
  DNAH7 WILD-TYPE 90 34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      4    2
  DNAH7 WILD-TYPE   90   34
     clus
vv    DNAH7 MUTATED DNAH7 WILD-TYPE
  NO              4              90
  YES             2              34
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DNAH7 MUTATED                                     6
  DNAH7 WILD-TYPE                                 124
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DNAH7 MUTATED                                       1
  DNAH7 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DNAH7 MUTATED                                                  0
  DNAH7 WILD-TYPE                                                2
D127V9, 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                          124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D127V10, continuous
D127V11, continuous
                 vv
clus              R0 R1 R2 RX
  DNAH7 MUTATED    6  0  0  0
  DNAH7 WILD-TYPE 73 50  4  3
D127V12, multiclass
    clus
vv   DNAH7 MUTATED DNAH7 WILD-TYPE
  R0             6              73
  R1             0              50
  R2             0               4
  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"
D127V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNAH7 MUTATED       0                         0     7
  DNAH7 WILD-TYPE     9                         5   121
D127V14, multiclass
                           clus
vv                          DNAH7 MUTATED DNAH7 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 7             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"
D127V15, binary
                 cls
clus               0  1
  DNAH7 MUTATED    0  7
  DNAH7 WILD-TYPE  5 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH7 MUTATED      0    7
  DNAH7 WILD-TYPE    5   98
                        clus
vv                       DNAH7 MUTATED DNAH7 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7              98
[1] 2 2
[1] FALSE

Clustering(128) Variable = MC3R MUTATION ANALYSIS
D128V1, survival
                sevent
clus2             0  1
  MC3R MUTATED    1  3
  MC3R WILD-TYPE 67 73
  MC3R MUTATED MC3R WILD-TYPE 
             4            140 
  MC3R MUTATED MC3R WILD-TYPE 
             3             73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-7891 TCGA-IB-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-8127 
       15.81        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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG 
       23.08        22.85        39.98        16.80        14.14        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  MC3R MUTATED MC3R WILD-TYPE 
          0.39           0.03 
  MC3R MUTATED MC3R WILD-TYPE 
         19.82          75.12 
  MC3R MUTATED MC3R WILD-TYPE 
        16.210         14.285 
[1] "0.4 - 19.8 (16.2)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.7"
D128V2, 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        3        7        23       101         3        4
D128V3, multiclass
           clus
vv          MC3R MUTATED MC3R WILD-TYPE
  STAGE IA             0              3
  STAGE IB             1              7
  STAGE IIA            0             23
  STAGE IIB            2            101
  STAGE III            1              3
  STAGE IV             0              4
[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   4  15   122
D128V4, multiclass
       clus
vv      MC3R MUTATED MC3R WILD-TYPE
  T1               0              4
  T2               1             15
  T3+T4            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"
D128V5, binary
                cls
clus               0   1
  MC3R MUTATED     1   3
  MC3R WILD-TYPE  36 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      1    3
  MC3R WILD-TYPE   36  105
   clus
vv  MC3R MUTATED MC3R WILD-TYPE
  0            1             36
  1            3            105
[1] 2 2
[1] FALSE
D128V6, binary
                cls
clus              0  1
  MC3R MUTATED    2  0
  MC3R WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      2    0
  MC3R WILD-TYPE   64    4
   clus
vv  MC3R MUTATED MC3R WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D128V7, binary
                cls
clus              0  1
  MC3R MUTATED    2  2
  MC3R WILD-TYPE 65 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      2    2
  MC3R WILD-TYPE   65   77
        clus
vv       MC3R MUTATED MC3R WILD-TYPE
  FEMALE            2             65
  MALE              2             77
[1] 2 2
[1] FALSE
D128V8, binary
                cls
clus              0  1
  MC3R MUTATED    3  1
  MC3R WILD-TYPE 91 35
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      3    1
  MC3R WILD-TYPE   91   35
     clus
vv    MC3R MUTATED MC3R WILD-TYPE
  NO             3             91
  YES            1             35
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MC3R MUTATED                                     3
  MC3R WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MC3R MUTATED                                       0
  MC3R WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MC3R MUTATED                                                  0
  MC3R WILD-TYPE                                                2
D128V9, multiclass
                                                  clus
vv                                                 MC3R MUTATED MC3R WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D128V10, continuous
[1] "Remove cluster labels:" "MC3R MUTATED"          
clus
  MC3R MUTATED MC3R WILD-TYPE 
             1             49 
    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-HV-AA8V     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-7887     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
    TCGA-YY-A8LH 
"MC3R WILD-TYPE" 
D128V11, continuous
[1] "Remove cluster labels:" "MC3R MUTATED"          
clus
  MC3R MUTATED MC3R WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"MC3R WILD-TYPE" "MC3R WILD-TYPE" "MC3R WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MC3R MUTATED    3  0  0  0
  MC3R WILD-TYPE 76 50  4  3
D128V12, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  R0            3             76
  R1            0             50
  R2            0              4
  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"
D128V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MC3R MUTATED       0                         0     3
  MC3R WILD-TYPE     9                         5   125
D128V14, multiclass
                           clus
vv                          MC3R MUTATED MC3R WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V15, binary
                cls
clus               0   1
  MC3R MUTATED     0   3
  MC3R WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      0    3
  MC3R WILD-TYPE    5  102
                        clus
vv                       MC3R MUTATED MC3R WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(129) Variable = FAM8A1 MUTATION ANALYSIS
D129V1, survival
                  sevent
clus2               0  1
  FAM8A1 MUTATED    3  1
  FAM8A1 WILD-TYPE 65 75
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               4              140 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               1               75 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       15.06        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
           12.95             0.03 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
           34.09            75.12 
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
          17.555           14.155 
[1] "12.9 - 34.1 (17.6)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "2.7"
D129V2, 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        2        8        22       102         4        3
D129V3, multiclass
           clus
vv          FAM8A1 MUTATED FAM8A1 WILD-TYPE
  STAGE IA               1                2
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              1              102
  STAGE III              0                4
  STAGE IV               1                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
  FAM8A1 MUTATED     1   0     3
  FAM8A1 WILD-TYPE   3  16   122
D129V4, multiclass
       clus
vv      FAM8A1 MUTATED FAM8A1 WILD-TYPE
  T1                 1                3
  T2                 0               16
  T3+T4              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"
D129V5, binary
                  cls
clus                 0   1
  FAM8A1 MUTATED     2   2
  FAM8A1 WILD-TYPE  35 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      2    2
  FAM8A1 WILD-TYPE   35  106
   clus
vv  FAM8A1 MUTATED FAM8A1 WILD-TYPE
  0              2               35
  1              2              106
[1] 2 2
[1] FALSE
D129V6, binary
                  cls
clus                0  1
  FAM8A1 MUTATED    2  1
  FAM8A1 WILD-TYPE 64  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      2    1
  FAM8A1 WILD-TYPE   64    3
   clus
vv  FAM8A1 MUTATED FAM8A1 WILD-TYPE
  0              2               64
  1              1                3
[1] 2 2
[1] FALSE
D129V7, binary
                  cls
clus                0  1
  FAM8A1 MUTATED    2  2
  FAM8A1 WILD-TYPE 65 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      2    2
  FAM8A1 WILD-TYPE   65   77
        clus
vv       FAM8A1 MUTATED FAM8A1 WILD-TYPE
  FEMALE              2               65
  MALE                2               77
[1] 2 2
[1] FALSE
D129V8, binary
                  cls
clus                0  1
  FAM8A1 MUTATED    1  3
  FAM8A1 WILD-TYPE 93 33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      1    3
  FAM8A1 WILD-TYPE   93   33
     clus
vv    FAM8A1 MUTATED FAM8A1 WILD-TYPE
  NO               1               93
  YES              3               33
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM8A1 MUTATED                                     4
  FAM8A1 WILD-TYPE                                 126
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM8A1 MUTATED                                       0
  FAM8A1 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM8A1 MUTATED                                                  0
  FAM8A1 WILD-TYPE                                                2
D129V9, 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                           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D129V10, continuous
[1] "Remove cluster labels:" "FAM8A1 MUTATED"        
clus
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               2               48 
      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-HV-AA8V 
"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-7887 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
D129V11, continuous
[1] "Remove cluster labels:" "FAM8A1 MUTATED"        
clus
  FAM8A1 MUTATED FAM8A1 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"FAM8A1 WILD-TYPE" "FAM8A1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  FAM8A1 MUTATED    1  3  0  0
  FAM8A1 WILD-TYPE 78 47  4  3
D129V12, multiclass
    clus
vv   FAM8A1 MUTATED FAM8A1 WILD-TYPE
  R0              1               78
  R1              3               47
  R2              0                4
  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"
D129V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM8A1 MUTATED       0                         0     3
  FAM8A1 WILD-TYPE     9                         5   125
D129V14, multiclass
                           clus
vv                          FAM8A1 MUTATED FAM8A1 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V15, binary
                  cls
clus                 0   1
  FAM8A1 MUTATED     0   2
  FAM8A1 WILD-TYPE   5 103
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM8A1 MUTATED      0    2
  FAM8A1 WILD-TYPE    5  103
                        clus
vv                       FAM8A1 MUTATED FAM8A1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2              103
[1] 2 2
[1] FALSE

Clustering(130) Variable = TGFBR1 MUTATION ANALYSIS
D130V1, survival
                  sevent
clus2               0  1
  TGFBR1 MUTATED    4  4
  TGFBR1 WILD-TYPE 64 72
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               8              136 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               4               72 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ 
       33.57        15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-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-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-A8RM 
       15.45        13.68         3.12        15.32         9.40        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E 
       17.26        23.08        22.85        39.98        16.80        14.14 
TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 
        0.39        13.81        12.99        12.03        16.37        31.27 
TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       23.67        11.51        12.76        15.35 

  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
            5.88             0.03 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
           75.12            71.74 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
          12.445           14.435 
[1] "5.9 - 75.1 (12.4)" "0.0 - 71.7 (14.4)"
[1] "hr=" "1.5"
D130V2, 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        3        8        23        95         4        4
D130V3, multiclass
           clus
vv          TGFBR1 MUTATED TGFBR1 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              8               95
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   117
D130V4, multiclass
       clus
vv      TGFBR1 MUTATED TGFBR1 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D130V5, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED     0   8
  TGFBR1 WILD-TYPE  37 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      0    8
  TGFBR1 WILD-TYPE   37  100
   clus
vv  TGFBR1 MUTATED TGFBR1 WILD-TYPE
  0              0               37
  1              8              100
[1] 2 2
[1] FALSE
D130V6, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    4  0
  TGFBR1 WILD-TYPE 62  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      4    0
  TGFBR1 WILD-TYPE   62    4
   clus
vv  TGFBR1 MUTATED TGFBR1 WILD-TYPE
  0              4               62
  1              0                4
[1] 2 2
[1] FALSE
D130V7, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    5  3
  TGFBR1 WILD-TYPE 62 76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      5    3
  TGFBR1 WILD-TYPE   62   76
        clus
vv       TGFBR1 MUTATED TGFBR1 WILD-TYPE
  FEMALE              5               62
  MALE                3               76
[1] 2 2
[1] FALSE
D130V8, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    4  3
  TGFBR1 WILD-TYPE 90 33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      4    3
  TGFBR1 WILD-TYPE   90   33
     clus
vv    TGFBR1 MUTATED TGFBR1 WILD-TYPE
  NO               4               90
  YES              3               33
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGFBR1 MUTATED                                     8
  TGFBR1 WILD-TYPE                                 122
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGFBR1 MUTATED                                       0
  TGFBR1 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGFBR1 MUTATED                                                  0
  TGFBR1 WILD-TYPE                                                2
D130V9, 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                           122
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D130V10, continuous
D130V11, continuous
                  vv
clus               R0 R1 R2 RX
  TGFBR1 MUTATED    7  0  0  0
  TGFBR1 WILD-TYPE 72 50  4  3
D130V12, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  R0              7               72
  R1              0               50
  R2              0                4
  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"
D130V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGFBR1 MUTATED       0                         0     8
  TGFBR1 WILD-TYPE     9                         5   120
D130V14, multiclass
                           clus
vv                          TGFBR1 MUTATED TGFBR1 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  8              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"
D130V15, binary
                  cls
clus                0  1
  TGFBR1 MUTATED    0  7
  TGFBR1 WILD-TYPE  5 98
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      0    7
  TGFBR1 WILD-TYPE    5   98
                        clus
vv                       TGFBR1 MUTATED TGFBR1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              7               98
[1] 2 2
[1] FALSE

Clustering(131) Variable = L1CAM MUTATION ANALYSIS
D131V1, survival
                 sevent
clus2              0  1
  L1CAM MUTATED    1  5
  L1CAM WILD-TYPE 67 71
  L1CAM MUTATED L1CAM WILD-TYPE 
              6             138 
  L1CAM MUTATED L1CAM WILD-TYPE 
              5              71 
$`L1CAM MUTATED`
TCGA-2J-AAB9 TCGA-HZ-7925 TCGA-HZ-A9TJ TCGA-IB-AAUO TCGA-US-A774 TCGA-US-A77E 
       20.61        20.19        19.82         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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-AAUP TCGA-IB-AAUQ 
        8.22        15.88         0.26         4.73        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-A776 
       15.32         9.40        24.23        17.26        23.08        39.98 
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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  L1CAM MUTATED L1CAM WILD-TYPE 
           7.86            0.03 
  L1CAM MUTATED L1CAM WILD-TYPE 
          22.85           75.12 
  L1CAM MUTATED L1CAM WILD-TYPE 
         20.005          14.005 
[1] "7.9 - 22.9 (20.0)" "0.0 - 75.1 (14.0)"
[1] "hr=" "1.3"
D131V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  L1CAM MUTATED          0        0         0         5         0        1
  L1CAM WILD-TYPE        3        8        23        98         4        3
D131V3, multiclass
           clus
vv          L1CAM MUTATED L1CAM WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              1               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     6
  L1CAM WILD-TYPE   4  16   119
D131V4, multiclass
       clus
vv      L1CAM MUTATED L1CAM WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D131V5, binary
                 cls
clus                0   1
  L1CAM MUTATED     1   5
  L1CAM WILD-TYPE  36 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      1    5
  L1CAM WILD-TYPE   36  103
   clus
vv  L1CAM MUTATED L1CAM WILD-TYPE
  0             1              36
  1             5             103
[1] 2 2
[1] FALSE
D131V6, binary
                 cls
clus               0  1
  L1CAM MUTATED    2  1
  L1CAM WILD-TYPE 64  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      2    1
  L1CAM WILD-TYPE   64    3
   clus
vv  L1CAM MUTATED L1CAM WILD-TYPE
  0             2              64
  1             1               3
[1] 2 2
[1] FALSE
D131V7, binary
                 cls
clus               0  1
  L1CAM MUTATED    3  3
  L1CAM WILD-TYPE 64 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      3    3
  L1CAM WILD-TYPE   64   76
        clus
vv       L1CAM MUTATED L1CAM WILD-TYPE
  FEMALE             3              64
  MALE               3              76
[1] 2 2
[1] FALSE
D131V8, binary
                 cls
clus               0  1
  L1CAM MUTATED    5  1
  L1CAM WILD-TYPE 89 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      5    1
  L1CAM WILD-TYPE   89   35
     clus
vv    L1CAM MUTATED L1CAM WILD-TYPE
  NO              5              89
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  L1CAM MUTATED                                     4
  L1CAM WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  L1CAM MUTATED                                       2
  L1CAM WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  L1CAM MUTATED                                                  0
  L1CAM WILD-TYPE                                                2
D131V9, multiclass
                                                  clus
vv                                                 L1CAM MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 L1CAM WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          126
  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"
D131V10, continuous
[1] "Remove cluster labels:" "L1CAM MUTATED"         
clus
  L1CAM MUTATED L1CAM WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-IB-AAUU      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-S4-A8RP      TCGA-XD-AAUL      TCGA-XN-A8T5 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-YY-A8LH 
"L1CAM WILD-TYPE" 
D131V11, continuous
[1] "Remove cluster labels:" "L1CAM MUTATED"         
clus
  L1CAM MUTATED L1CAM WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  L1CAM MUTATED    4  2  0  0
  L1CAM WILD-TYPE 75 48  4  3
D131V12, multiclass
    clus
vv   L1CAM MUTATED L1CAM WILD-TYPE
  R0             4              75
  R1             2              48
  R2             0               4
  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"
D131V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  L1CAM MUTATED       0                         0     6
  L1CAM WILD-TYPE     9                         5   122
D131V14, multiclass
                           clus
vv                          L1CAM MUTATED L1CAM WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             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"
D131V15, binary
                 cls
clus                0   1
  L1CAM MUTATED     0   5
  L1CAM WILD-TYPE   5 100
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      0    5
  L1CAM WILD-TYPE    5  100
                        clus
vv                       L1CAM MUTATED L1CAM WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             100
[1] 2 2
[1] FALSE

Clustering(132) Variable = LCP2 MUTATION ANALYSIS
D132V1, survival
                sevent
clus2             0  1
  LCP2 MUTATED    1  2
  LCP2 WILD-TYPE 67 74
  LCP2 MUTATED LCP2 WILD-TYPE 
             3            141 
  LCP2 MUTATED LCP2 WILD-TYPE 
             2             74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAZ 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  LCP2 MUTATED LCP2 WILD-TYPE 
         19.82           0.03 
  LCP2 MUTATED LCP2 WILD-TYPE 
         75.12          71.74 
  LCP2 MUTATED LCP2 WILD-TYPE 
         20.19          14.14 
[1] "19.8 - 75.1 (20.2)" "0.0 - 71.7 (14.1)" 
[1] "hr=" "2.1"
D132V2, 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        3        8        23       100         4        4
D132V3, multiclass
           clus
vv          LCP2 MUTATED LCP2 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   122
D132V4, multiclass
       clus
vv      LCP2 MUTATED LCP2 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D132V5, binary
                cls
clus               0   1
  LCP2 MUTATED     0   3
  LCP2 WILD-TYPE  37 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP2 MUTATED      0    3
  LCP2 WILD-TYPE   37  105
   clus
vv  LCP2 MUTATED LCP2 WILD-TYPE
  0            0             37
  1            3            105
[1] 2 2
[1] FALSE
D132V6, binary
                cls
clus              0  1
  LCP2 MUTATED    1  0
  LCP2 WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP2 MUTATED      1    0
  LCP2 WILD-TYPE   65    4
   clus
vv  LCP2 MUTATED LCP2 WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D132V7, binary
                cls
clus              0  1
  LCP2 MUTATED    1  2
  LCP2 WILD-TYPE 66 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP2 MUTATED      1    2
  LCP2 WILD-TYPE   66   77
        clus
vv       LCP2 MUTATED LCP2 WILD-TYPE
  FEMALE            1             66
  MALE              2             77
[1] 2 2
[1] FALSE
D132V8, binary
                cls
clus              0  1
  LCP2 MUTATED    3  0
  LCP2 WILD-TYPE 91 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP2 MUTATED      3    0
  LCP2 WILD-TYPE   91   36
     clus
vv    LCP2 MUTATED LCP2 WILD-TYPE
  NO             3             91
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LCP2 MUTATED                                     3
  LCP2 WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LCP2 MUTATED                                       0
  LCP2 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LCP2 MUTATED                                                  0
  LCP2 WILD-TYPE                                                2
D132V9, multiclass
                                                  clus
vv                                                 LCP2 MUTATED LCP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D132V10, continuous
[1] "Remove cluster labels:" "LCP2 MUTATED"          
clus
  LCP2 MUTATED LCP2 WILD-TYPE 
             1             49 
    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-HV-AA8V     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-7887     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-YY-A8LH 
"LCP2 WILD-TYPE" 
D132V11, continuous
[1] "Remove cluster labels:" "LCP2 MUTATED"          
clus
  LCP2 MUTATED LCP2 WILD-TYPE 
             1             39 
    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-XN-A8T5     TCGA-YY-A8LH 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  LCP2 MUTATED    2  0  0  0
  LCP2 WILD-TYPE 77 50  4  3
D132V12, multiclass
[1] "Remove cluster labels:" "LCP2 MUTATED"          
clus
  LCP2 MUTATED LCP2 WILD-TYPE 
             2            134 
    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-HV-A5A6     TCGA-HV-A7OL 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-HV-AA8V     TCGA-HV-AA8X     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-HZ-A9TJ     TCGA-IB-7644     TCGA-IB-7645     TCGA-IB-7646 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7647     TCGA-IB-7649     TCGA-IB-7652     TCGA-IB-7885 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7886     TCGA-IB-7887     TCGA-IB-7888     TCGA-IB-7889 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-7890     TCGA-IB-7891     TCGA-IB-7893     TCGA-IB-7897 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SO     TCGA-IB-A5SP 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-A5SQ     TCGA-IB-A5SS     TCGA-IB-A5ST     TCGA-IB-A6UF 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7LX     TCGA-IB-A7M4     TCGA-IB-AAUM 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-AAUN     TCGA-IB-AAUO     TCGA-IB-AAUP     TCGA-IB-AAUQ 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-IB-AAUR     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A8F3     TCGA-LB-A9Q5     TCGA-M8-A5N4 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-Q3-A5QY     TCGA-Q3-AA2A     TCGA-RB-A7B8 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-RB-AA9M     TCGA-S4-A8RM     TCGA-S4-A8RO     TCGA-S4-A8RP 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-US-A774     TCGA-US-A776     TCGA-US-A779     TCGA-US-A77E 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-US-A77G     TCGA-XD-AAUG     TCGA-XD-AAUH     TCGA-XD-AAUI 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-XN-A8T3     TCGA-XN-A8T5     TCGA-YB-A89D 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
    TCGA-YY-A8LH     TCGA-Z5-AAPL 
"LCP2 WILD-TYPE" "LCP2 WILD-TYPE" 
D132V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LCP2 MUTATED       0                         0     3
  LCP2 WILD-TYPE     9                         5   125
D132V14, multiclass
                           clus
vv                          LCP2 MUTATED LCP2 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                3            125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V15, binary
                cls
clus               0   1
  LCP2 MUTATED     0   3
  LCP2 WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCP2 MUTATED      0    3
  LCP2 WILD-TYPE    5  102
                        clus
vv                       LCP2 MUTATED LCP2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(133) Variable = ZNF358 MUTATION ANALYSIS
D133V1, survival
                  sevent
clus2               0  1
  ZNF358 MUTATED    1  3
  ZNF358 WILD-TYPE 67 73
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               4              140 
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               3               73 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
       21.60         5.26        10.85         0.23        19.82        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZNF358 MUTATED ZNF358 WILD-TYPE 
            1.08             0.03 
  ZNF358 MUTATED ZNF358 WILD-TYPE 
           19.82            75.12 
  ZNF358 MUTATED ZNF358 WILD-TYPE 
          14.990           14.285 
[1] "1.1 - 19.8 (15.0)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.8"
D133V2, 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        3        8        23       100         3        4
D133V3, multiclass
           clus
vv          ZNF358 MUTATED ZNF358 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              1                3
  STAGE IV               0                4
[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   4  16   121
D133V4, multiclass
       clus
vv      ZNF358 MUTATED ZNF358 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D133V5, binary
                  cls
clus                 0   1
  ZNF358 MUTATED     1   3
  ZNF358 WILD-TYPE  36 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF358 MUTATED      1    3
  ZNF358 WILD-TYPE   36  105
   clus
vv  ZNF358 MUTATED ZNF358 WILD-TYPE
  0              1               36
  1              3              105
[1] 2 2
[1] FALSE
D133V6, binary
                  cls
clus                0  1
  ZNF358 MUTATED    1  0
  ZNF358 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF358 MUTATED      1    0
  ZNF358 WILD-TYPE   65    4
   clus
vv  ZNF358 MUTATED ZNF358 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D133V7, binary
                  cls
clus                0  1
  ZNF358 MUTATED    3  1
  ZNF358 WILD-TYPE 64 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF358 MUTATED      3    1
  ZNF358 WILD-TYPE   64   78
        clus
vv       ZNF358 MUTATED ZNF358 WILD-TYPE
  FEMALE              3               64
  MALE                1               78
[1] 2 2
[1] FALSE
D133V8, binary
                  cls
clus                0  1
  ZNF358 MUTATED    2  0
  ZNF358 WILD-TYPE 92 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF358 MUTATED      2    0
  ZNF358 WILD-TYPE   92   36
     clus
vv    ZNF358 MUTATED ZNF358 WILD-TYPE
  NO               2               92
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF358 MUTATED                                     3
  ZNF358 WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF358 MUTATED                                       1
  ZNF358 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF358 MUTATED                                                  0
  ZNF358 WILD-TYPE                                                2
D133V9, 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                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D133V10, continuous
[1] "Remove cluster labels:" "ZNF358 MUTATED"        
clus
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               2               48 
      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-HV-AA8V       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-7887 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
D133V11, continuous
[1] "Remove cluster labels:" "ZNF358 MUTATED"        
clus
  ZNF358 MUTATED ZNF358 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"ZNF358 WILD-TYPE" "ZNF358 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF358 MUTATED    2  1  0  1
  ZNF358 WILD-TYPE 77 49  4  2
D133V12, multiclass
    clus
vv   ZNF358 MUTATED ZNF358 WILD-TYPE
  R0              2               77
  R1              1               49
  R2              0                4
  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"
D133V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF358 MUTATED       0                         1     3
  ZNF358 WILD-TYPE     9                         4   125
D133V14, multiclass
                           clus
vv                          ZNF358 MUTATED ZNF358 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V15, binary
                  cls
clus                 0   1
  ZNF358 MUTATED     0   3
  ZNF358 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF358 MUTATED      0    3
  ZNF358 WILD-TYPE    5  102
                        clus
vv                       ZNF358 MUTATED ZNF358 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(134) Variable = KCNE1 MUTATION ANALYSIS
D134V1, survival
                 sevent
clus2              0  1
  KCNE1 MUTATED    1  3
  KCNE1 WILD-TYPE 67 73
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              4             140 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  KCNE1 MUTATED KCNE1 WILD-TYPE 
          10.98            0.03 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
          41.33           75.12 
  KCNE1 MUTATED KCNE1 WILD-TYPE 
         20.005          14.155 
[1] "11.0 - 41.3 (20.0)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "1"  
D134V2, 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        3        8        23        99         4        4
D134V3, multiclass
           clus
vv          KCNE1 MUTATED KCNE1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   121
D134V4, multiclass
       clus
vv      KCNE1 MUTATED KCNE1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D134V5, binary
                 cls
clus                0   1
  KCNE1 MUTATED     0   4
  KCNE1 WILD-TYPE  37 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      0    4
  KCNE1 WILD-TYPE   37  104
   clus
vv  KCNE1 MUTATED KCNE1 WILD-TYPE
  0             0              37
  1             4             104
[1] 2 2
[1] FALSE
D134V6, binary
                 cls
clus               0  1
  KCNE1 MUTATED    3  0
  KCNE1 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      3    0
  KCNE1 WILD-TYPE   63    4
   clus
vv  KCNE1 MUTATED KCNE1 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D134V7, binary
                 cls
clus               0  1
  KCNE1 MUTATED    2  2
  KCNE1 WILD-TYPE 65 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      2    2
  KCNE1 WILD-TYPE   65   77
        clus
vv       KCNE1 MUTATED KCNE1 WILD-TYPE
  FEMALE             2              65
  MALE               2              77
[1] 2 2
[1] FALSE
D134V8, binary
                 cls
clus               0  1
  KCNE1 MUTATED    4  0
  KCNE1 WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      4    0
  KCNE1 WILD-TYPE   90   36
     clus
vv    KCNE1 MUTATED KCNE1 WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KCNE1 MUTATED                                     3
  KCNE1 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KCNE1 MUTATED                                       1
  KCNE1 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KCNE1 MUTATED                                                  0
  KCNE1 WILD-TYPE                                                2
D134V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D134V10, continuous
[1] "Remove cluster labels:" "KCNE1 MUTATED"         
clus
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
D134V11, continuous
[1] "Remove cluster labels:" "KCNE1 MUTATED"         
clus
  KCNE1 MUTATED KCNE1 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"KCNE1 WILD-TYPE" "KCNE1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  KCNE1 MUTATED    4  0  0  0
  KCNE1 WILD-TYPE 75 50  4  3
D134V12, multiclass
    clus
vv   KCNE1 MUTATED KCNE1 WILD-TYPE
  R0             4              75
  R1             0              50
  R2             0               4
  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"
D134V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNE1 MUTATED       0                         0     4
  KCNE1 WILD-TYPE     9                         5   124
D134V14, multiclass
                           clus
vv                          KCNE1 MUTATED KCNE1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V15, binary
                 cls
clus                0   1
  KCNE1 MUTATED     0   3
  KCNE1 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNE1 MUTATED      0    3
  KCNE1 WILD-TYPE    5  102
                        clus
vv                       KCNE1 MUTATED KCNE1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(135) Variable = OR1N2 MUTATION ANALYSIS
D135V1, survival
                 sevent
clus2              0  1
  OR1N2 MUTATED    1  4
  OR1N2 WILD-TYPE 67 72
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              5             139 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              4              72 
$`OR1N2 MUTATED`
TCGA-3E-AAAZ TCGA-IB-7651 TCGA-IB-7888 TCGA-IB-AAUO TCGA-XN-A8T5 
       71.74        19.82        43.79         7.86        23.67 

$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04         3.62        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-AAUP TCGA-IB-AAUQ 
        8.22        15.88         0.26         4.73        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       12.03        16.37        31.27        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  OR1N2 MUTATED OR1N2 WILD-TYPE 
           7.86            0.03 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
          71.74           75.12 
  OR1N2 MUTATED OR1N2 WILD-TYPE 
          23.67           14.14 
[1] "7.9 - 71.7 (23.7)" "0.0 - 75.1 (14.1)"
[1] "hr=" "1.5"
D135V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OR1N2 MUTATED          0        1         2         2         0        0
  OR1N2 WILD-TYPE        3        7        21       101         4        4
D135V3, multiclass
           clus
vv          OR1N2 MUTATED OR1N2 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             2              21
  STAGE IIB             2             101
  STAGE III             0               4
  STAGE IV              0               4
[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   1     4
  OR1N2 WILD-TYPE   4  15   121
D135V4, multiclass
       clus
vv      OR1N2 MUTATED OR1N2 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D135V5, binary
                 cls
clus                0   1
  OR1N2 MUTATED     3   2
  OR1N2 WILD-TYPE  34 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      3    2
  OR1N2 WILD-TYPE   34  106
   clus
vv  OR1N2 MUTATED OR1N2 WILD-TYPE
  0             3              34
  1             2             106
[1] 2 2
[1] FALSE
D135V6, binary
                 cls
clus               0  1
  OR1N2 MUTATED    4  0
  OR1N2 WILD-TYPE 62  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      4    0
  OR1N2 WILD-TYPE   62    4
   clus
vv  OR1N2 MUTATED OR1N2 WILD-TYPE
  0             4              62
  1             0               4
[1] 2 2
[1] FALSE
D135V7, binary
                 cls
clus               0  1
  OR1N2 MUTATED    4  1
  OR1N2 WILD-TYPE 63 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      4    1
  OR1N2 WILD-TYPE   63   78
        clus
vv       OR1N2 MUTATED OR1N2 WILD-TYPE
  FEMALE             4              63
  MALE               1              78
[1] 2 2
[1] FALSE
D135V8, binary
                 cls
clus               0  1
  OR1N2 MUTATED    3  1
  OR1N2 WILD-TYPE 91 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      3    1
  OR1N2 WILD-TYPE   91   35
     clus
vv    OR1N2 MUTATED OR1N2 WILD-TYPE
  NO              3              91
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR1N2 MUTATED                                     4
  OR1N2 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR1N2 MUTATED                                       1
  OR1N2 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR1N2 MUTATED                                                  0
  OR1N2 WILD-TYPE                                                2
D135V9, multiclass
                                                  clus
vv                                                 OR1N2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 OR1N2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D135V10, continuous
[1] "Remove cluster labels:" "OR1N2 MUTATED"         
clus
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-YY-A8LH 
"OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" "OR1N2 WILD-TYPE" 
D135V11, continuous
[1] "Remove cluster labels:" "OR1N2 MUTATED"         
clus
  OR1N2 MUTATED OR1N2 WILD-TYPE 
              2              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  2  0  0
  OR1N2 WILD-TYPE 77 48  4  3
D135V12, multiclass
    clus
vv   OR1N2 MUTATED OR1N2 WILD-TYPE
  R0             2              77
  R1             2              48
  R2             0               4
  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"
D135V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR1N2 MUTATED       0                         1     4
  OR1N2 WILD-TYPE     9                         4   124
D135V14, multiclass
                           clus
vv                          OR1N2 MUTATED OR1N2 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V15, binary
                 cls
clus                0   1
  OR1N2 MUTATED     2   3
  OR1N2 WILD-TYPE   3 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1N2 MUTATED      2    3
  OR1N2 WILD-TYPE    3  102
                        clus
vv                       OR1N2 MUTATED OR1N2 WILD-TYPE
  HISPANIC OR LATINO                 2               3
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(136) Variable = FLVCR1 MUTATION ANALYSIS
D136V1, survival
                  sevent
clus2               0  1
  FLVCR1 MUTATED    1  2
  FLVCR1 WILD-TYPE 67 74
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               3              141 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               2               74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       33.57        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
        6.38        21.60         5.26        10.85         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
            1.08             0.03 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
           19.82            75.12 
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
           15.06            14.17 
[1] "1.1 - 19.8 (15.1)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.8"
D136V2, 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        3        8        23       100         4        4
D136V3, multiclass
           clus
vv          FLVCR1 MUTATED FLVCR1 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   122
D136V4, multiclass
       clus
vv      FLVCR1 MUTATED FLVCR1 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D136V5, binary
                  cls
clus                 0   1
  FLVCR1 MUTATED     0   3
  FLVCR1 WILD-TYPE  37 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      0    3
  FLVCR1 WILD-TYPE   37  105
   clus
vv  FLVCR1 MUTATED FLVCR1 WILD-TYPE
  0              0               37
  1              3              105
[1] 2 2
[1] FALSE
D136V6, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    1  0
  FLVCR1 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      1    0
  FLVCR1 WILD-TYPE   65    4
   clus
vv  FLVCR1 MUTATED FLVCR1 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D136V7, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    2  1
  FLVCR1 WILD-TYPE 65 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      2    1
  FLVCR1 WILD-TYPE   65   78
        clus
vv       FLVCR1 MUTATED FLVCR1 WILD-TYPE
  FEMALE              2               65
  MALE                1               78
[1] 2 2
[1] FALSE
D136V8, binary
                  cls
clus                0  1
  FLVCR1 MUTATED    2  0
  FLVCR1 WILD-TYPE 92 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      2    0
  FLVCR1 WILD-TYPE   92   36
     clus
vv    FLVCR1 MUTATED FLVCR1 WILD-TYPE
  NO               2               92
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FLVCR1 MUTATED                                     2
  FLVCR1 WILD-TYPE                                 128
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FLVCR1 MUTATED                                       1
  FLVCR1 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FLVCR1 MUTATED                                                  0
  FLVCR1 WILD-TYPE                                                2
D136V9, 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                           128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D136V10, continuous
[1] "Remove cluster labels:" "FLVCR1 MUTATED"        
clus
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               2               48 
      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-HV-AA8V       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-7887 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
D136V11, continuous
[1] "Remove cluster labels:" "FLVCR1 MUTATED"        
clus
  FLVCR1 MUTATED FLVCR1 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"FLVCR1 WILD-TYPE" "FLVCR1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  FLVCR1 MUTATED    3  0  0  0
  FLVCR1 WILD-TYPE 76 50  4  3
D136V12, multiclass
    clus
vv   FLVCR1 MUTATED FLVCR1 WILD-TYPE
  R0              3               76
  R1              0               50
  R2              0                4
  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"
D136V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FLVCR1 MUTATED       0                         0     3
  FLVCR1 WILD-TYPE     9                         5   125
D136V14, multiclass
                           clus
vv                          FLVCR1 MUTATED FLVCR1 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V15, binary
                  cls
clus                 0   1
  FLVCR1 MUTATED     0   3
  FLVCR1 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FLVCR1 MUTATED      0    3
  FLVCR1 WILD-TYPE    5  102
                        clus
vv                       FLVCR1 MUTATED FLVCR1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(137) Variable = BTN2A1 MUTATION ANALYSIS
D137V1, survival
                  sevent
clus2               0  1
  BTN2A1 MUTATED    2  1
  BTN2A1 WILD-TYPE 66 75
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               3              141 
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               1               75 
$`BTN2A1 MUTATED`
TCGA-3A-A9IH TCGA-HZ-A4BK TCGA-IB-7651 
       33.57        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        42.31        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        58.98        43.50        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        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
        6.38         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
           19.82             0.03 
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
           33.57            75.12 
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
           21.60            14.14 
[1] "19.8 - 33.6 (21.6)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "2.7"
D137V2, 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        2        8        23       101         4        4
D137V3, multiclass
           clus
vv          BTN2A1 MUTATED BTN2A1 WILD-TYPE
  STAGE IA               1                2
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              2              101
  STAGE III              0                4
  STAGE IV               0                4
[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   3  16   123
D137V4, multiclass
       clus
vv      BTN2A1 MUTATED BTN2A1 WILD-TYPE
  T1                 1                3
  T2                 0               16
  T3+T4              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"
D137V5, binary
                  cls
clus                 0   1
  BTN2A1 MUTATED     1   2
  BTN2A1 WILD-TYPE  36 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A1 MUTATED      1    2
  BTN2A1 WILD-TYPE   36  106
   clus
vv  BTN2A1 MUTATED BTN2A1 WILD-TYPE
  0              1               36
  1              2              106
[1] 2 2
[1] FALSE
D137V6, binary
                  cls
clus                0  1
  BTN2A1 MUTATED    1  0
  BTN2A1 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A1 MUTATED      1    0
  BTN2A1 WILD-TYPE   65    4
   clus
vv  BTN2A1 MUTATED BTN2A1 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D137V7, binary
                  cls
clus                0  1
  BTN2A1 MUTATED    2  1
  BTN2A1 WILD-TYPE 65 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A1 MUTATED      2    1
  BTN2A1 WILD-TYPE   65   78
        clus
vv       BTN2A1 MUTATED BTN2A1 WILD-TYPE
  FEMALE              2               65
  MALE                1               78
[1] 2 2
[1] FALSE
D137V8, binary
                  cls
clus                0  1
  BTN2A1 MUTATED    2  1
  BTN2A1 WILD-TYPE 92 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A1 MUTATED      2    1
  BTN2A1 WILD-TYPE   92   35
     clus
vv    BTN2A1 MUTATED BTN2A1 WILD-TYPE
  NO               2               92
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BTN2A1 MUTATED                                     2
  BTN2A1 WILD-TYPE                                 128
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BTN2A1 MUTATED                                       1
  BTN2A1 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BTN2A1 MUTATED                                                  0
  BTN2A1 WILD-TYPE                                                2
D137V9, 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                           128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D137V10, continuous
[1] "Remove cluster labels:" "BTN2A1 MUTATED"        
clus
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               1               49 
      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-HV-AA8V       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-7887       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-A5SS       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-S4-A8RP       TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
      TCGA-YY-A8LH 
"BTN2A1 WILD-TYPE" 
D137V11, continuous
[1] "Remove cluster labels:" "BTN2A1 MUTATED"        
clus
  BTN2A1 MUTATED BTN2A1 WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" "BTN2A1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  BTN2A1 MUTATED    2  1  0  0
  BTN2A1 WILD-TYPE 77 49  4  3
D137V12, multiclass
    clus
vv   BTN2A1 MUTATED BTN2A1 WILD-TYPE
  R0              2               77
  R1              1               49
  R2              0                4
  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"
D137V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTN2A1 MUTATED       0                         0     3
  BTN2A1 WILD-TYPE     9                         5   125
D137V14, multiclass
                           clus
vv                          BTN2A1 MUTATED BTN2A1 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V15, binary
                  cls
clus                 0   1
  BTN2A1 MUTATED     0   3
  BTN2A1 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTN2A1 MUTATED      0    3
  BTN2A1 WILD-TYPE    5  102
                        clus
vv                       BTN2A1 MUTATED BTN2A1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(138) Variable = PAPSS2 MUTATION ANALYSIS
D138V1, survival
                  sevent
clus2               0  1
  PAPSS2 MUTATED    2  2
  PAPSS2 WILD-TYPE 66 74
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               4              140 
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               2               74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-HZ-A8P1 
       10.13         6.38         5.26        10.85         1.08         0.23 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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-AA2A 
       12.46        10.29        19.20         8.78        15.45         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
            3.62             0.03 
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
           21.60            75.12 
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
          16.750           14.285 
[1] "3.6 - 21.6 (16.8)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1"  
D138V2, 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        3        8        23        99         4        4
D138V3, multiclass
           clus
vv          PAPSS2 MUTATED PAPSS2 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              4               99
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   121
D138V4, multiclass
       clus
vv      PAPSS2 MUTATED PAPSS2 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D138V5, binary
                  cls
clus                 0   1
  PAPSS2 MUTATED     0   4
  PAPSS2 WILD-TYPE  37 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPSS2 MUTATED      0    4
  PAPSS2 WILD-TYPE   37  104
   clus
vv  PAPSS2 MUTATED PAPSS2 WILD-TYPE
  0              0               37
  1              4              104
[1] 2 2
[1] FALSE
D138V6, binary
                  cls
clus                0  1
  PAPSS2 MUTATED    2  0
  PAPSS2 WILD-TYPE 64  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPSS2 MUTATED      2    0
  PAPSS2 WILD-TYPE   64    4
   clus
vv  PAPSS2 MUTATED PAPSS2 WILD-TYPE
  0              2               64
  1              0                4
[1] 2 2
[1] FALSE
D138V7, binary
                  cls
clus                0  1
  PAPSS2 MUTATED    2  2
  PAPSS2 WILD-TYPE 65 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPSS2 MUTATED      2    2
  PAPSS2 WILD-TYPE   65   77
        clus
vv       PAPSS2 MUTATED PAPSS2 WILD-TYPE
  FEMALE              2               65
  MALE                2               77
[1] 2 2
[1] FALSE
D138V8, binary
                  cls
clus                0  1
  PAPSS2 MUTATED    3  1
  PAPSS2 WILD-TYPE 91 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPSS2 MUTATED      3    1
  PAPSS2 WILD-TYPE   91   35
     clus
vv    PAPSS2 MUTATED PAPSS2 WILD-TYPE
  NO               3               91
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PAPSS2 MUTATED                                     3
  PAPSS2 WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PAPSS2 MUTATED                                       1
  PAPSS2 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PAPSS2 MUTATED                                                  0
  PAPSS2 WILD-TYPE                                                2
D138V9, 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                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D138V10, continuous
[1] "Remove cluster labels:" "PAPSS2 MUTATED"        
clus
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               2               48 
      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-HV-AA8V       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-IB-AAUU       TCGA-LB-A7SX 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
D138V11, continuous
[1] "Remove cluster labels:" "PAPSS2 MUTATED"        
clus
  PAPSS2 MUTATED PAPSS2 WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" "PAPSS2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PAPSS2 MUTATED    2  2  0  0
  PAPSS2 WILD-TYPE 77 48  4  3
D138V12, multiclass
    clus
vv   PAPSS2 MUTATED PAPSS2 WILD-TYPE
  R0              2               77
  R1              2               48
  R2              0                4
  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"
D138V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAPSS2 MUTATED       0                         0     4
  PAPSS2 WILD-TYPE     9                         5   124
D138V14, multiclass
                           clus
vv                          PAPSS2 MUTATED PAPSS2 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V15, binary
                  cls
clus                 0   1
  PAPSS2 MUTATED     0   4
  PAPSS2 WILD-TYPE   5 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAPSS2 MUTATED      0    4
  PAPSS2 WILD-TYPE    5  101
                        clus
vv                       PAPSS2 MUTATED PAPSS2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              101
[1] 2 2
[1] FALSE

Clustering(139) Variable = PBRM1 MUTATION ANALYSIS
D139V1, survival
                 sevent
clus2              0  1
  PBRM1 MUTATED    2  3
  PBRM1 WILD-TYPE 66 73
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              5             139 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              3              73 
$`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        15.35 

$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       19.82        12.95         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-A8F3 
        6.02        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-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH 
       66.28 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.23            0.03 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          49.38           75.12 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          15.35           14.17 
[1] "0.2 - 49.4 (15.3)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1"  
D139V2, 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        3        7        22       100         4        4
D139V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             1              22
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  15   121
D139V4, multiclass
       clus
vv      PBRM1 MUTATED PBRM1 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D139V5, binary
                 cls
clus                0   1
  PBRM1 MUTATED     2   3
  PBRM1 WILD-TYPE  35 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      2    3
  PBRM1 WILD-TYPE   35  105
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             2              35
  1             3             105
[1] 2 2
[1] FALSE
D139V6, binary
                 cls
clus               0  1
  PBRM1 MUTATED    3  0
  PBRM1 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      3    0
  PBRM1 WILD-TYPE   63    4
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D139V7, binary
                 cls
clus               0  1
  PBRM1 MUTATED    4  1
  PBRM1 WILD-TYPE 63 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      4    1
  PBRM1 WILD-TYPE   63   78
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE             4              63
  MALE               1              78
[1] 2 2
[1] FALSE
D139V8, binary
                 cls
clus               0  1
  PBRM1 MUTATED    4  0
  PBRM1 WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      4    0
  PBRM1 WILD-TYPE   90   36
     clus
vv    PBRM1 MUTATED PBRM1 WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PBRM1 MUTATED                                     5
  PBRM1 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PBRM1 MUTATED                                       0
  PBRM1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PBRM1 MUTATED                                                  0
  PBRM1 WILD-TYPE                                                2
D139V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D139V10, continuous
D139V11, continuous
                 vv
clus              R0 R1 R2 RX
  PBRM1 MUTATED    4  1  0  0
  PBRM1 WILD-TYPE 75 49  4  3
D139V12, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  R0             4              75
  R1             1              49
  R2             0               4
  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"
D139V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED       0                         1     3
  PBRM1 WILD-TYPE     9                         4   125
D139V14, multiclass
                           clus
vv                          PBRM1 MUTATED PBRM1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V15, binary
                 cls
clus                0   1
  PBRM1 MUTATED     0   4
  PBRM1 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      0    4
  PBRM1 WILD-TYPE    5  101
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(140) Variable = CYTH4 MUTATION ANALYSIS
D140V1, survival
                 sevent
clus2              0  1
  CYTH4 MUTATED    0  3
  CYTH4 WILD-TYPE 68 73
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              3             141 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       20.19        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 
       19.82        23.80        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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG 
       23.08        22.85        39.98        16.80        14.14        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  CYTH4 MUTATED CYTH4 WILD-TYPE 
           0.39            0.03 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
          17.03           75.12 
  CYTH4 MUTATED CYTH4 WILD-TYPE 
           3.62           14.40 
[1] "0.4 - 17.0 (3.6)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "4.9"
D140V2, 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        3        8        23       100         4        4
D140V3, multiclass
           clus
vv          CYTH4 MUTATED CYTH4 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D140V4, multiclass
       clus
vv      CYTH4 MUTATED CYTH4 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D140V5, binary
                 cls
clus                0   1
  CYTH4 MUTATED     0   3
  CYTH4 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      0    3
  CYTH4 WILD-TYPE   37  105
   clus
vv  CYTH4 MUTATED CYTH4 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D140V6, binary
                 cls
clus               0  1
  CYTH4 MUTATED    1  0
  CYTH4 WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      1    0
  CYTH4 WILD-TYPE   65    4
   clus
vv  CYTH4 MUTATED CYTH4 WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D140V7, binary
                 cls
clus               0  1
  CYTH4 MUTATED    1  2
  CYTH4 WILD-TYPE 66 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      1    2
  CYTH4 WILD-TYPE   66   77
        clus
vv       CYTH4 MUTATED CYTH4 WILD-TYPE
  FEMALE             1              66
  MALE               2              77
[1] 2 2
[1] FALSE
D140V8, binary
                 cls
clus               0  1
  CYTH4 MUTATED    2  0
  CYTH4 WILD-TYPE 92 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      2    0
  CYTH4 WILD-TYPE   92   36
     clus
vv    CYTH4 MUTATED CYTH4 WILD-TYPE
  NO              2              92
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CYTH4 MUTATED                                     3
  CYTH4 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CYTH4 MUTATED                                       0
  CYTH4 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CYTH4 MUTATED                                                  0
  CYTH4 WILD-TYPE                                                2
D140V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D140V10, continuous
[1] "Remove cluster labels:" "CYTH4 MUTATED"         
clus
  CYTH4 MUTATED CYTH4 WILD-TYPE 
              1              49 
     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-HV-AA8V      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" "CYTH4 WILD-TYPE" 
     TCGA-YY-A8LH 
"CYTH4 WILD-TYPE" 
D140V11, continuous
                 vv
clus              R0 R1 R2 RX
  CYTH4 MUTATED    1  1  0  1
  CYTH4 WILD-TYPE 78 49  4  2
D140V12, multiclass
    clus
vv   CYTH4 MUTATED CYTH4 WILD-TYPE
  R0             1              78
  R1             1              49
  R2             0               4
  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"
D140V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYTH4 MUTATED       0                         1     2
  CYTH4 WILD-TYPE     9                         4   126
D140V14, multiclass
                           clus
vv                          CYTH4 MUTATED CYTH4 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 2             126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V15, binary
                 cls
clus                0   1
  CYTH4 MUTATED     0   3
  CYTH4 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTH4 MUTATED      0    3
  CYTH4 WILD-TYPE    5  102
                        clus
vv                       CYTH4 MUTATED CYTH4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(141) Variable = ANKRD49 MUTATION ANALYSIS
D141V1, survival
                   sevent
clus2                0  1
  ANKRD49 MUTATED    0  3
  ANKRD49 WILD-TYPE 68 73
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3               141 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                3                73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
       20.19        17.03        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
             3.62              0.03 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
            19.82             75.12 
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
             3.95             14.40 
[1] "3.6 - 19.8 (4.0)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "3.7"
D141V2, 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        3        8        23       100         4        4
D141V3, multiclass
           clus
vv          ANKRD49 MUTATED ANKRD49 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               0                23
  STAGE IIB               3               100
  STAGE III               0                 4
  STAGE IV                0                 4
[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   4  16   122
D141V4, multiclass
       clus
vv      ANKRD49 MUTATED ANKRD49 WILD-TYPE
  T1                  0                 4
  T2                  0                16
  T3+T4               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"
D141V5, binary
                   cls
clus                  0   1
  ANKRD49 MUTATED     0   3
  ANKRD49 WILD-TYPE  37 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      0    3
  ANKRD49 WILD-TYPE   37  105
   clus
vv  ANKRD49 MUTATED ANKRD49 WILD-TYPE
  0               0                37
  1               3               105
[1] 2 2
[1] FALSE
D141V6, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    2  0
  ANKRD49 WILD-TYPE 64  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      2    0
  ANKRD49 WILD-TYPE   64    4
   clus
vv  ANKRD49 MUTATED ANKRD49 WILD-TYPE
  0               2                64
  1               0                 4
[1] 2 2
[1] FALSE
D141V7, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    2  1
  ANKRD49 WILD-TYPE 65 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      2    1
  ANKRD49 WILD-TYPE   65   78
        clus
vv       ANKRD49 MUTATED ANKRD49 WILD-TYPE
  FEMALE               2                65
  MALE                 1                78
[1] 2 2
[1] FALSE
D141V8, binary
                   cls
clus                 0  1
  ANKRD49 MUTATED    3  0
  ANKRD49 WILD-TYPE 91 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      3    0
  ANKRD49 WILD-TYPE   91   36
     clus
vv    ANKRD49 MUTATED ANKRD49 WILD-TYPE
  NO                3                91
  YES               0                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANKRD49 MUTATED                                     3
  ANKRD49 WILD-TYPE                                 127
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANKRD49 MUTATED                                       0
  ANKRD49 WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANKRD49 MUTATED                                                  0
  ANKRD49 WILD-TYPE                                                2
D141V9, 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                            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D141V10, continuous
[1] "Remove cluster labels:" "ANKRD49 MUTATED"       
clus
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                2                48 
       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-HV-AA8V        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-IB-AAUU        TCGA-LB-A7SX 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
D141V11, continuous
[1] "Remove cluster labels:" "ANKRD49 MUTATED"       
clus
  ANKRD49 MUTATED ANKRD49 WILD-TYPE 
                1                39 
       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-XN-A8T5        TCGA-YY-A8LH 
"ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" "ANKRD49 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  ANKRD49 MUTATED    1  2  0  0
  ANKRD49 WILD-TYPE 78 48  4  3
D141V12, multiclass
    clus
vv   ANKRD49 MUTATED ANKRD49 WILD-TYPE
  R0               1                78
  R1               2                48
  R2               0                 4
  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"
D141V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD49 MUTATED       0                         0     3
  ANKRD49 WILD-TYPE     9                         5   125
D141V14, multiclass
                           clus
vv                          ANKRD49 MUTATED ANKRD49 WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V15, binary
                   cls
clus                  0   1
  ANKRD49 MUTATED     0   3
  ANKRD49 WILD-TYPE   5 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD49 MUTATED      0    3
  ANKRD49 WILD-TYPE    5  102
                        clus
vv                       ANKRD49 MUTATED ANKRD49 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               3               102
[1] 2 2
[1] FALSE

Clustering(142) Variable = CMYA5 MUTATION ANALYSIS
D142V1, survival
                 sevent
clus2              0  1
  CMYA5 MUTATED    2  6
  CMYA5 WILD-TYPE 66 70
  CMYA5 MUTATED CMYA5 WILD-TYPE 
              8             136 
  CMYA5 MUTATED CMYA5 WILD-TYPE 
              6              70 
$`CMYA5 MUTATED`
TCGA-2J-AABA TCGA-2J-AABH TCGA-HV-AA8V TCGA-HZ-8002 TCGA-IB-7649 TCGA-IB-7651 
       19.96        42.31        30.25        12.03        15.35        19.82 
TCGA-IB-AAUQ TCGA-US-A779 
        6.02        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        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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 
       19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        12.95        49.38 
TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
        4.77        21.90        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-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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G 
       17.26        23.08        22.85        39.98        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  CMYA5 MUTATED CMYA5 WILD-TYPE 
           6.02            0.03 
  CMYA5 MUTATED CMYA5 WILD-TYPE 
          42.31           75.12 
  CMYA5 MUTATED CMYA5 WILD-TYPE 
          18.31           13.99 
[1] "6.0 - 42.3 (18.3)" "0.0 - 75.1 (14.0)"
[1] "hr=" "1.2"
D142V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CMYA5 MUTATED          0        0         1         7         0        0
  CMYA5 WILD-TYPE        3        8        22        96         4        4
D142V3, multiclass
           clus
vv          CMYA5 MUTATED CMYA5 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             7              96
  STAGE III             0               4
  STAGE IV              0               4
[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     8
  CMYA5 WILD-TYPE   4  16   117
D142V4, multiclass
       clus
vv      CMYA5 MUTATED CMYA5 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D142V5, binary
                 cls
clus                0   1
  CMYA5 MUTATED     1   7
  CMYA5 WILD-TYPE  36 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMYA5 MUTATED      1    7
  CMYA5 WILD-TYPE   36  101
   clus
vv  CMYA5 MUTATED CMYA5 WILD-TYPE
  0             1              36
  1             7             101
[1] 2 2
[1] FALSE
D142V6, binary
                 cls
clus               0  1
  CMYA5 MUTATED    5  0
  CMYA5 WILD-TYPE 61  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMYA5 MUTATED      5    0
  CMYA5 WILD-TYPE   61    4
   clus
vv  CMYA5 MUTATED CMYA5 WILD-TYPE
  0             5              61
  1             0               4
[1] 2 2
[1] FALSE
D142V7, binary
                 cls
clus               0  1
  CMYA5 MUTATED    3  5
  CMYA5 WILD-TYPE 64 74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMYA5 MUTATED      3    5
  CMYA5 WILD-TYPE   64   74
        clus
vv       CMYA5 MUTATED CMYA5 WILD-TYPE
  FEMALE             3              64
  MALE               5              74
[1] 2 2
[1] FALSE
D142V8, binary
                 cls
clus               0  1
  CMYA5 MUTATED    7  0
  CMYA5 WILD-TYPE 87 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMYA5 MUTATED      7    0
  CMYA5 WILD-TYPE   87   36
     clus
vv    CMYA5 MUTATED CMYA5 WILD-TYPE
  NO              7              87
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CMYA5 MUTATED                                     7
  CMYA5 WILD-TYPE                                 123
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CMYA5 MUTATED                                       1
  CMYA5 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CMYA5 MUTATED                                                  0
  CMYA5 WILD-TYPE                                                2
D142V9, multiclass
                                                  clus
vv                                                 CMYA5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CMYA5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D142V10, continuous
D142V11, continuous
                 vv
clus              R0 R1 R2 RX
  CMYA5 MUTATED    4  3  1  0
  CMYA5 WILD-TYPE 75 47  3  3
D142V12, multiclass
    clus
vv   CMYA5 MUTATED CMYA5 WILD-TYPE
  R0             4              75
  R1             3              47
  R2             1               3
  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"
D142V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CMYA5 MUTATED       1                         0     6
  CMYA5 WILD-TYPE     8                         5   122
D142V14, multiclass
                           clus
vv                          CMYA5 MUTATED CMYA5 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             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"
D142V15, binary
                 cls
clus                0   1
  CMYA5 MUTATED     0   4
  CMYA5 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CMYA5 MUTATED      0    4
  CMYA5 WILD-TYPE    5  101
                        clus
vv                       CMYA5 MUTATED CMYA5 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(143) Variable = PHF15 MUTATION ANALYSIS
D143V1, survival
                 sevent
clus2              0  1
  PHF15 MUTATED    2  2
  PHF15 WILD-TYPE 66 74
  PHF15 MUTATED PHF15 WILD-TYPE 
              4             140 
  PHF15 MUTATED PHF15 WILD-TYPE 
              2              74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-A6UG 
       17.16        12.00        15.85         7.20        15.12         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-US-A774 
        3.12        15.32         9.40        24.23        17.26        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  PHF15 MUTATED PHF15 WILD-TYPE 
          19.82            0.03 
  PHF15 MUTATED PHF15 WILD-TYPE 
          23.08           75.12 
  PHF15 MUTATED PHF15 WILD-TYPE 
          21.39           13.99 
[1] "19.8 - 23.1 (21.4)" "0.0 - 75.1 (14.0)" 
[1] "hr=" "1.8"
D143V2, 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        3        8        23        99         4        4
D143V3, multiclass
           clus
vv          PHF15 MUTATED PHF15 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   121
D143V4, multiclass
       clus
vv      PHF15 MUTATED PHF15 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D143V5, binary
                 cls
clus                0   1
  PHF15 MUTATED     0   4
  PHF15 WILD-TYPE  37 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF15 MUTATED      0    4
  PHF15 WILD-TYPE   37  104
   clus
vv  PHF15 MUTATED PHF15 WILD-TYPE
  0             0              37
  1             4             104
[1] 2 2
[1] FALSE
D143V6, binary
                 cls
clus               0  1
  PHF15 MUTATED    3  0
  PHF15 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF15 MUTATED      3    0
  PHF15 WILD-TYPE   63    4
   clus
vv  PHF15 MUTATED PHF15 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D143V7, binary
                 cls
clus               0  1
  PHF15 MUTATED    3  1
  PHF15 WILD-TYPE 64 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF15 MUTATED      3    1
  PHF15 WILD-TYPE   64   78
        clus
vv       PHF15 MUTATED PHF15 WILD-TYPE
  FEMALE             3              64
  MALE               1              78
[1] 2 2
[1] FALSE
D143V8, binary
                 cls
clus               0  1
  PHF15 MUTATED    3  1
  PHF15 WILD-TYPE 91 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF15 MUTATED      3    1
  PHF15 WILD-TYPE   91   35
     clus
vv    PHF15 MUTATED PHF15 WILD-TYPE
  NO              3              91
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHF15 MUTATED                                     4
  PHF15 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHF15 MUTATED                                       0
  PHF15 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHF15 MUTATED                                                  0
  PHF15 WILD-TYPE                                                2
D143V9, 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                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D143V10, continuous
D143V11, continuous
[1] "Remove cluster labels:" "PHF15 MUTATED"         
clus
  PHF15 MUTATED PHF15 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"PHF15 WILD-TYPE" "PHF15 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  PHF15 MUTATED    3  1  0  0
  PHF15 WILD-TYPE 76 49  4  3
D143V12, multiclass
    clus
vv   PHF15 MUTATED PHF15 WILD-TYPE
  R0             3              76
  R1             1              49
  R2             0               4
  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"
D143V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF15 MUTATED       0                         0     4
  PHF15 WILD-TYPE     9                         5   124
D143V14, multiclass
                           clus
vv                          PHF15 MUTATED PHF15 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V15, binary
                 cls
clus                0   1
  PHF15 MUTATED     0   3
  PHF15 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF15 MUTATED      0    3
  PHF15 WILD-TYPE    5  102
                        clus
vv                       PHF15 MUTATED PHF15 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(144) Variable = RSPO1 MUTATION ANALYSIS
D144V1, survival
                 sevent
clus2              0  1
  RSPO1 MUTATED    1  2
  RSPO1 WILD-TYPE 67 74
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              3             141 
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              2              74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  RSPO1 MUTATED RSPO1 WILD-TYPE 
           7.50            0.03 
  RSPO1 MUTATED RSPO1 WILD-TYPE 
          19.82           75.12 
  RSPO1 MUTATED RSPO1 WILD-TYPE 
          10.98           14.40 
[1] "7.5 - 19.8 (11.0)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.7"
D144V2, 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        3        8        23       100         4        4
D144V3, multiclass
           clus
vv          RSPO1 MUTATED RSPO1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  15   123
D144V4, multiclass
       clus
vv      RSPO1 MUTATED RSPO1 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D144V5, binary
                 cls
clus                0   1
  RSPO1 MUTATED     0   3
  RSPO1 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO1 MUTATED      0    3
  RSPO1 WILD-TYPE   37  105
   clus
vv  RSPO1 MUTATED RSPO1 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D144V6, binary
                 cls
clus               0  1
  RSPO1 MUTATED    2  0
  RSPO1 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO1 MUTATED      2    0
  RSPO1 WILD-TYPE   64    4
   clus
vv  RSPO1 MUTATED RSPO1 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D144V7, binary
                 cls
clus               0  1
  RSPO1 MUTATED    2  1
  RSPO1 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO1 MUTATED      2    1
  RSPO1 WILD-TYPE   65   78
        clus
vv       RSPO1 MUTATED RSPO1 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D144V8, binary
                 cls
clus               0  1
  RSPO1 MUTATED    2  1
  RSPO1 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO1 MUTATED      2    1
  RSPO1 WILD-TYPE   92   35
     clus
vv    RSPO1 MUTATED RSPO1 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RSPO1 MUTATED                                     2
  RSPO1 WILD-TYPE                                 128
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RSPO1 MUTATED                                       1
  RSPO1 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RSPO1 MUTATED                                                  0
  RSPO1 WILD-TYPE                                                2
D144V9, 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                          128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D144V10, continuous
[1] "Remove cluster labels:" "RSPO1 MUTATED"         
clus
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              2              48 
     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-HV-AA8V 
"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-7887 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
D144V11, continuous
[1] "Remove cluster labels:" "RSPO1 MUTATED"         
clus
  RSPO1 MUTATED RSPO1 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"RSPO1 WILD-TYPE" "RSPO1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  RSPO1 MUTATED    3  0  0  0
  RSPO1 WILD-TYPE 76 50  4  3
D144V12, multiclass
    clus
vv   RSPO1 MUTATED RSPO1 WILD-TYPE
  R0             3              76
  R1             0              50
  R2             0               4
  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"
D144V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RSPO1 MUTATED       0                         0     3
  RSPO1 WILD-TYPE     9                         5   125
D144V14, multiclass
                           clus
vv                          RSPO1 MUTATED RSPO1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V15, binary
                 cls
clus                0   1
  RSPO1 MUTATED     0   2
  RSPO1 WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO1 MUTATED      0    2
  RSPO1 WILD-TYPE    5  103
                        clus
vv                       RSPO1 MUTATED RSPO1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(145) Variable = ASH1L MUTATION ANALYSIS
D145V1, survival
                 sevent
clus2              0  1
  ASH1L MUTATED    4  2
  ASH1L WILD-TYPE 64 74
  ASH1L MUTATED ASH1L WILD-TYPE 
              6             138 
  ASH1L MUTATED ASH1L WILD-TYPE 
              2              74 
$`ASH1L MUTATED`
TCGA-3A-A9IH TCGA-HZ-7925 TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-7885 TCGA-YB-A89D 
       33.57        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        42.31        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        58.98        43.50        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        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
       21.60         5.26        10.85         0.23        19.82        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       16.37        31.27        23.67        12.76        66.28        15.35 

  ASH1L MUTATED ASH1L WILD-TYPE 
           1.08            0.03 
  ASH1L MUTATED ASH1L WILD-TYPE 
          41.33           75.12 
  ASH1L MUTATED ASH1L WILD-TYPE 
         20.005          14.155 
[1] "1.1 - 41.3 (20.0)" "0.0 - 75.1 (14.2)"
[1] "hr=" "2.1"
D145V2, 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        2        8        23        98         4        4
D145V3, multiclass
           clus
vv          ASH1L MUTATED ASH1L WILD-TYPE
  STAGE IA              1               2
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              0               4
[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   3  16   120
D145V4, multiclass
       clus
vv      ASH1L MUTATED ASH1L WILD-TYPE
  T1                1               3
  T2                0              16
  T3+T4             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"
D145V5, binary
                 cls
clus                0   1
  ASH1L MUTATED     1   5
  ASH1L WILD-TYPE  36 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      1    5
  ASH1L WILD-TYPE   36  103
   clus
vv  ASH1L MUTATED ASH1L WILD-TYPE
  0             1              36
  1             5             103
[1] 2 2
[1] FALSE
D145V6, binary
                 cls
clus               0  1
  ASH1L MUTATED    2  0
  ASH1L WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      2    0
  ASH1L WILD-TYPE   64    4
   clus
vv  ASH1L MUTATED ASH1L WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D145V7, binary
                 cls
clus               0  1
  ASH1L MUTATED    4  2
  ASH1L WILD-TYPE 63 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      4    2
  ASH1L WILD-TYPE   63   77
        clus
vv       ASH1L MUTATED ASH1L WILD-TYPE
  FEMALE             4              63
  MALE               2              77
[1] 2 2
[1] FALSE
D145V8, binary
                 cls
clus               0  1
  ASH1L MUTATED    4  1
  ASH1L WILD-TYPE 90 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      4    1
  ASH1L WILD-TYPE   90   35
     clus
vv    ASH1L MUTATED ASH1L WILD-TYPE
  NO              4              90
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ASH1L MUTATED                                     5
  ASH1L WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ASH1L MUTATED                                       1
  ASH1L WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ASH1L MUTATED                                                  0
  ASH1L WILD-TYPE                                                2
D145V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D145V10, continuous
D145V11, continuous
                 vv
clus              R0 R1 R2 RX
  ASH1L MUTATED    6  0  0  0
  ASH1L WILD-TYPE 73 50  4  3
D145V12, multiclass
    clus
vv   ASH1L MUTATED ASH1L WILD-TYPE
  R0             6              73
  R1             0              50
  R2             0               4
  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"
D145V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASH1L MUTATED       0                         0     6
  ASH1L WILD-TYPE     9                         5   122
D145V14, multiclass
                           clus
vv                          ASH1L MUTATED ASH1L WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 6             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"
D145V15, binary
                 cls
clus               0  1
  ASH1L MUTATED    0  6
  ASH1L WILD-TYPE  5 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      0    6
  ASH1L WILD-TYPE    5   99
                        clus
vv                       ASH1L MUTATED ASH1L WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             6              99
[1] 2 2
[1] FALSE

Clustering(146) Variable = BVES MUTATION ANALYSIS
D146V1, survival
                sevent
clus2             0  1
  BVES MUTATED    2  2
  BVES WILD-TYPE 66 74
  BVES MUTATED BVES WILD-TYPE 
             4            140 
  BVES MUTATED BVES WILD-TYPE 
             2             74 
$`BVES MUTATED`
TCGA-2J-AABR TCGA-IB-7646 TCGA-IB-7651 TCGA-XD-AAUL 
       14.40         4.77        19.82        16.37 

$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       19.82        12.95        49.38        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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  BVES MUTATED BVES WILD-TYPE 
          4.77           0.03 
  BVES MUTATED BVES WILD-TYPE 
         19.82          75.12 
  BVES MUTATED BVES WILD-TYPE 
        15.385         14.155 
[1] "4.8 - 19.8 (15.4)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.1"
D146V2, 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        3        8        21       101         4        4
D146V3, multiclass
           clus
vv          BVES MUTATED BVES WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            2             21
  STAGE IIB            2            101
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   121
D146V4, multiclass
       clus
vv      BVES MUTATED BVES WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D146V5, binary
                cls
clus               0   1
  BVES MUTATED     2   2
  BVES WILD-TYPE  35 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  BVES MUTATED      2    2
  BVES WILD-TYPE   35  106
   clus
vv  BVES MUTATED BVES WILD-TYPE
  0            2             35
  1            2            106
[1] 2 2
[1] FALSE
D146V6, binary
                cls
clus              0  1
  BVES MUTATED    3  0
  BVES WILD-TYPE 63  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BVES MUTATED      3    0
  BVES WILD-TYPE   63    4
   clus
vv  BVES MUTATED BVES WILD-TYPE
  0            3             63
  1            0              4
[1] 2 2
[1] FALSE
D146V7, binary
                cls
clus              0  1
  BVES MUTATED    2  2
  BVES WILD-TYPE 65 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  BVES MUTATED      2    2
  BVES WILD-TYPE   65   77
        clus
vv       BVES MUTATED BVES WILD-TYPE
  FEMALE            2             65
  MALE              2             77
[1] 2 2
[1] FALSE
D146V8, binary
                cls
clus              0  1
  BVES MUTATED    4  0
  BVES WILD-TYPE 90 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BVES MUTATED      4    0
  BVES WILD-TYPE   90   36
     clus
vv    BVES MUTATED BVES WILD-TYPE
  NO             4             90
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BVES MUTATED                                     4
  BVES WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BVES MUTATED                                       0
  BVES WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BVES MUTATED                                                  0
  BVES WILD-TYPE                                                2
D146V9, multiclass
                                                  clus
vv                                                 BVES MUTATED BVES WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D146V10, continuous
[1] "Remove cluster labels:" "BVES MUTATED"          
clus
  BVES MUTATED BVES WILD-TYPE 
             2             48 
    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-HV-AA8V     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-7887     TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-A5SS     TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-IB-AAUQ     TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
    TCGA-S4-A8RP     TCGA-US-A774     TCGA-XN-A8T5     TCGA-YY-A8LH 
"BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" "BVES WILD-TYPE" 
D146V11, continuous
[1] "Remove cluster labels:" "BVES MUTATED"          
clus
  BVES MUTATED BVES WILD-TYPE 
             2             38 
    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-XN-A8T5     TCGA-YY-A8LH 
"BVES WILD-TYPE" "BVES WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  BVES MUTATED    3  1  0  0
  BVES WILD-TYPE 76 49  4  3
D146V12, multiclass
    clus
vv   BVES MUTATED BVES WILD-TYPE
  R0            3             76
  R1            1             49
  R2            0              4
  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"
D146V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BVES MUTATED       0                         0     4
  BVES WILD-TYPE     9                         5   124
D146V14, multiclass
                           clus
vv                          BVES MUTATED BVES WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V15, binary
                cls
clus               0   1
  BVES MUTATED     0   3
  BVES WILD-TYPE   5 102
[1] "tbl2"
                cls
clus             [,1] [,2]
  BVES MUTATED      0    3
  BVES WILD-TYPE    5  102
                        clus
vv                       BVES MUTATED BVES WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            102
[1] 2 2
[1] FALSE

Clustering(147) Variable = DDX4 MUTATION ANALYSIS
D147V1, survival
                sevent
clus2             0  1
  DDX4 MUTATED    2  3
  DDX4 WILD-TYPE 66 73
  DDX4 MUTATED DDX4 WILD-TYPE 
             5            139 
  DDX4 MUTATED DDX4 WILD-TYPE 
             3             73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 TCGA-HZ-8317 
       23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 
       21.60         5.26        10.85         0.23        19.82        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  DDX4 MUTATED DDX4 WILD-TYPE 
          1.08           0.03 
  DDX4 MUTATED DDX4 WILD-TYPE 
         41.33          75.12 
  DDX4 MUTATED DDX4 WILD-TYPE 
         19.82          14.14 
[1] "1.1 - 41.3 (19.8)" "0.0 - 75.1 (14.1)"
[1] "hr=" "1.1"
D147V2, 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        3        8        23        98         4        4
D147V3, multiclass
           clus
vv          DDX4 MUTATED DDX4 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            5             98
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   120
D147V4, multiclass
       clus
vv      DDX4 MUTATED DDX4 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D147V5, binary
                cls
clus               0   1
  DDX4 MUTATED     0   5
  DDX4 WILD-TYPE  37 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX4 MUTATED      0    5
  DDX4 WILD-TYPE   37  103
   clus
vv  DDX4 MUTATED DDX4 WILD-TYPE
  0            0             37
  1            5            103
[1] 2 2
[1] FALSE
D147V6, binary
                cls
clus              0  1
  DDX4 MUTATED    2  0
  DDX4 WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX4 MUTATED      2    0
  DDX4 WILD-TYPE   64    4
   clus
vv  DDX4 MUTATED DDX4 WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D147V7, binary
                cls
clus              0  1
  DDX4 MUTATED    3  2
  DDX4 WILD-TYPE 64 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX4 MUTATED      3    2
  DDX4 WILD-TYPE   64   77
        clus
vv       DDX4 MUTATED DDX4 WILD-TYPE
  FEMALE            3             64
  MALE              2             77
[1] 2 2
[1] FALSE
D147V8, binary
                cls
clus              0  1
  DDX4 MUTATED    3  0
  DDX4 WILD-TYPE 91 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX4 MUTATED      3    0
  DDX4 WILD-TYPE   91   36
     clus
vv    DDX4 MUTATED DDX4 WILD-TYPE
  NO             3             91
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DDX4 MUTATED                                     4
  DDX4 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DDX4 MUTATED                                       1
  DDX4 WILD-TYPE                                    12
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DDX4 MUTATED                                                  0
  DDX4 WILD-TYPE                                                2
D147V9, multiclass
                                                  clus
vv                                                 DDX4 MUTATED DDX4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             12
  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"
D147V10, continuous
D147V11, continuous
                vv
clus             R0 R1 R2 RX
  DDX4 MUTATED    4  0  0  1
  DDX4 WILD-TYPE 75 50  4  2
D147V12, multiclass
    clus
vv   DDX4 MUTATED DDX4 WILD-TYPE
  R0            4             75
  R1            0             50
  R2            0              4
  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"
D147V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDX4 MUTATED       0                         1     4
  DDX4 WILD-TYPE     9                         4   124
D147V14, multiclass
                           clus
vv                          DDX4 MUTATED DDX4 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            1              4
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V15, binary
                cls
clus               0   1
  DDX4 MUTATED     0   5
  DDX4 WILD-TYPE   5 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX4 MUTATED      0    5
  DDX4 WILD-TYPE    5  100
                        clus
vv                       DDX4 MUTATED DDX4 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            5            100
[1] 2 2
[1] FALSE

Clustering(148) Variable = TEKT4 MUTATION ANALYSIS
D148V1, survival
                 sevent
clus2              0  1
  TEKT4 MUTATED    3  3
  TEKT4 WILD-TYPE 65 73
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              6             138 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
              3              73 
$`TEKT4 MUTATED`
TCGA-2J-AABR TCGA-3E-AAAZ TCGA-FB-A78T TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-7888 
       14.40        71.74         0.03         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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
        5.26        10.85         0.23        19.82        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 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  TEKT4 MUTATED TEKT4 WILD-TYPE 
           0.03            0.13 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
          71.74           75.12 
  TEKT4 MUTATED TEKT4 WILD-TYPE 
         17.110          14.155 
[1] "0.0 - 71.7 (17.1)" "0.1 - 75.1 (14.2)"
[1] "hr=" "1.7"
D148V2, 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        3        8        20       100         4        4
D148V3, multiclass
           clus
vv          TEKT4 MUTATED TEKT4 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             3              20
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   119
D148V4, multiclass
       clus
vv      TEKT4 MUTATED TEKT4 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D148V5, binary
                 cls
clus                0   1
  TEKT4 MUTATED     3   3
  TEKT4 WILD-TYPE  34 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      3    3
  TEKT4 WILD-TYPE   34  105
   clus
vv  TEKT4 MUTATED TEKT4 WILD-TYPE
  0             3              34
  1             3             105
[1] 2 2
[1] FALSE
D148V6, binary
                 cls
clus               0  1
  TEKT4 MUTATED    4  0
  TEKT4 WILD-TYPE 62  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      4    0
  TEKT4 WILD-TYPE   62    4
   clus
vv  TEKT4 MUTATED TEKT4 WILD-TYPE
  0             4              62
  1             0               4
[1] 2 2
[1] FALSE
D148V7, binary
                 cls
clus               0  1
  TEKT4 MUTATED    5  1
  TEKT4 WILD-TYPE 62 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      5    1
  TEKT4 WILD-TYPE   62   78
        clus
vv       TEKT4 MUTATED TEKT4 WILD-TYPE
  FEMALE             5              62
  MALE               1              78
[1] 2 2
[1] FALSE
D148V8, binary
                 cls
clus               0  1
  TEKT4 MUTATED    3  0
  TEKT4 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      3    0
  TEKT4 WILD-TYPE   91   36
     clus
vv    TEKT4 MUTATED TEKT4 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TEKT4 MUTATED                                     5
  TEKT4 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TEKT4 MUTATED                                       1
  TEKT4 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TEKT4 MUTATED                                                  0
  TEKT4 WILD-TYPE                                                2
D148V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D148V10, continuous
D148V11, continuous
                 vv
clus              R0 R1 R2 RX
  TEKT4 MUTATED    5  0  0  0
  TEKT4 WILD-TYPE 74 50  4  3
D148V12, multiclass
    clus
vv   TEKT4 MUTATED TEKT4 WILD-TYPE
  R0             5              74
  R1             0              50
  R2             0               4
  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"
D148V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TEKT4 MUTATED       0                         1     5
  TEKT4 WILD-TYPE     9                         4   123
D148V14, multiclass
                           clus
vv                          TEKT4 MUTATED TEKT4 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 5             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"
D148V15, binary
                 cls
clus                0   1
  TEKT4 MUTATED     1   4
  TEKT4 WILD-TYPE   4 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEKT4 MUTATED      1    4
  TEKT4 WILD-TYPE    4  101
                        clus
vv                       TEKT4 MUTATED TEKT4 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(149) Variable = WWP2 MUTATION ANALYSIS
D149V1, survival
                sevent
clus2             0  1
  WWP2 MUTATED    2  2
  WWP2 WILD-TYPE 66 74
  WWP2 MUTATED WWP2 WILD-TYPE 
             4            140 
  WWP2 MUTATED WWP2 WILD-TYPE 
             2             74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         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-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ 
        6.38        21.60         5.26         1.08         0.23        19.82 
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-AAUP 
        1.35         8.22        15.88         0.26         4.73        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        39.98        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  WWP2 MUTATED WWP2 WILD-TYPE 
          7.86           0.03 
  WWP2 MUTATED WWP2 WILD-TYPE 
         21.70          75.12 
  WWP2 MUTATED WWP2 WILD-TYPE 
        12.495         14.435 
[1] "7.9 - 21.7 (12.5)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.2"
D149V2, 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        3        8        23        98         4        4
D149V3, multiclass
           clus
vv          WWP2 MUTATED WWP2 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            5             98
  STAGE III            0              4
  STAGE IV             0              4
[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   4  15   121
D149V4, multiclass
       clus
vv      WWP2 MUTATED WWP2 WILD-TYPE
  T1               0              4
  T2               1             15
  T3+T4            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"
D149V5, binary
                cls
clus               0   1
  WWP2 MUTATED     0   5
  WWP2 WILD-TYPE  37 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWP2 MUTATED      0    5
  WWP2 WILD-TYPE   37  103
   clus
vv  WWP2 MUTATED WWP2 WILD-TYPE
  0            0             37
  1            5            103
[1] 2 2
[1] FALSE
D149V6, binary
                cls
clus              0  1
  WWP2 MUTATED    1  0
  WWP2 WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWP2 MUTATED      1    0
  WWP2 WILD-TYPE   65    4
   clus
vv  WWP2 MUTATED WWP2 WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D149V7, binary
                cls
clus              0  1
  WWP2 MUTATED    3  2
  WWP2 WILD-TYPE 64 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWP2 MUTATED      3    2
  WWP2 WILD-TYPE   64   77
        clus
vv       WWP2 MUTATED WWP2 WILD-TYPE
  FEMALE            3             64
  MALE              2             77
[1] 2 2
[1] FALSE
D149V8, binary
                cls
clus              0  1
  WWP2 MUTATED    3  1
  WWP2 WILD-TYPE 91 35
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWP2 MUTATED      3    1
  WWP2 WILD-TYPE   91   35
     clus
vv    WWP2 MUTATED WWP2 WILD-TYPE
  NO             3             91
  YES            1             35
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WWP2 MUTATED                                     3
  WWP2 WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WWP2 MUTATED                                       2
  WWP2 WILD-TYPE                                    11
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WWP2 MUTATED                                                  0
  WWP2 WILD-TYPE                                                2
D149V9, multiclass
                                                  clus
vv                                                 WWP2 MUTATED WWP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2             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"
D149V10, continuous
D149V11, continuous
                vv
clus             R0 R1 R2 RX
  WWP2 MUTATED    2  3  0  0
  WWP2 WILD-TYPE 77 47  4  3
D149V12, multiclass
    clus
vv   WWP2 MUTATED WWP2 WILD-TYPE
  R0            2             77
  R1            3             47
  R2            0              4
  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"
D149V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WWP2 MUTATED       0                         0     5
  WWP2 WILD-TYPE     9                         5   123
D149V14, multiclass
                           clus
vv                          WWP2 MUTATED WWP2 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                5            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"
D149V15, binary
                cls
clus               0   1
  WWP2 MUTATED     1   4
  WWP2 WILD-TYPE   4 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWP2 MUTATED      1    4
  WWP2 WILD-TYPE    4  101
                        clus
vv                       WWP2 MUTATED WWP2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(150) Variable = DHX35 MUTATION ANALYSIS
D150V1, survival
                 sevent
clus2              0  1
  DHX35 MUTATED    1  3
  DHX35 WILD-TYPE 67 73
  DHX35 MUTATED DHX35 WILD-TYPE 
              4             140 
  DHX35 MUTATED DHX35 WILD-TYPE 
              3              73 
$`DHX35 MUTATED`
TCGA-2J-AAB1 TCGA-FB-A5VM TCGA-IB-7885 TCGA-IB-7887 
        2.17        16.37        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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 
       23.80         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  DHX35 MUTATED DHX35 WILD-TYPE 
           2.17            0.03 
  DHX35 MUTATED DHX35 WILD-TYPE 
          41.33           75.12 
  DHX35 MUTATED DHX35 WILD-TYPE 
          9.995          14.285 
[1] "2.2 - 41.3 (10.0)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.7"
D150V2, 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        3        7        23       100         4        4
D150V3, multiclass
           clus
vv          DHX35 MUTATED DHX35 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              1               7
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  15   122
D150V4, multiclass
       clus
vv      DHX35 MUTATED DHX35 WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4             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"
D150V5, binary
                 cls
clus                0   1
  DHX35 MUTATED     1   3
  DHX35 WILD-TYPE  36 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      1    3
  DHX35 WILD-TYPE   36  105
   clus
vv  DHX35 MUTATED DHX35 WILD-TYPE
  0             1              36
  1             3             105
[1] 2 2
[1] FALSE
D150V6, binary
                 cls
clus               0  1
  DHX35 MUTATED    4  0
  DHX35 WILD-TYPE 62  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      4    0
  DHX35 WILD-TYPE   62    4
   clus
vv  DHX35 MUTATED DHX35 WILD-TYPE
  0             4              62
  1             0               4
[1] 2 2
[1] FALSE
D150V7, binary
                 cls
clus               0  1
  DHX35 MUTATED    2  2
  DHX35 WILD-TYPE 65 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      2    2
  DHX35 WILD-TYPE   65   77
        clus
vv       DHX35 MUTATED DHX35 WILD-TYPE
  FEMALE             2              65
  MALE               2              77
[1] 2 2
[1] FALSE
D150V8, binary
                 cls
clus               0  1
  DHX35 MUTATED    4  0
  DHX35 WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      4    0
  DHX35 WILD-TYPE   90   36
     clus
vv    DHX35 MUTATED DHX35 WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DHX35 MUTATED                                     3
  DHX35 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DHX35 MUTATED                                       1
  DHX35 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DHX35 MUTATED                                                  0
  DHX35 WILD-TYPE                                                2
D150V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D150V10, continuous
D150V11, continuous
                 vv
clus              R0 R1 R2 RX
  DHX35 MUTATED    3  1  0  0
  DHX35 WILD-TYPE 76 49  4  3
D150V12, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  R0             3              76
  R1             1              49
  R2             0               4
  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"
D150V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DHX35 MUTATED       0                         0     4
  DHX35 WILD-TYPE     9                         5   124
D150V14, multiclass
                           clus
vv                          DHX35 MUTATED DHX35 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V15, binary
                 cls
clus                0   1
  DHX35 MUTATED     0   3
  DHX35 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      0    3
  DHX35 WILD-TYPE    5  102
                        clus
vv                       DHX35 MUTATED DHX35 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(151) Variable = WDR36 MUTATION ANALYSIS
D151V1, survival
                 sevent
clus2              0  1
  WDR36 MUTATED    0  3
  WDR36 WILD-TYPE 68 73
  WDR36 MUTATED WDR36 WILD-TYPE 
              3             141 
  WDR36 MUTATED WDR36 WILD-TYPE 
              3              73 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  WDR36 MUTATED WDR36 WILD-TYPE 
          15.35            0.03 
  WDR36 MUTATED WDR36 WILD-TYPE 
          20.61           75.12 
  WDR36 MUTATED WDR36 WILD-TYPE 
          20.19           14.14 
[1] "15.3 - 20.6 (20.2)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "1.5"
D151V2, 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        3        8        23       100         4        4
D151V3, multiclass
           clus
vv          WDR36 MUTATED WDR36 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D151V4, multiclass
       clus
vv      WDR36 MUTATED WDR36 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D151V5, binary
                 cls
clus                0   1
  WDR36 MUTATED     0   3
  WDR36 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR36 MUTATED      0    3
  WDR36 WILD-TYPE   37  105
   clus
vv  WDR36 MUTATED WDR36 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D151V6, binary
                 cls
clus               0  1
  WDR36 MUTATED    2  0
  WDR36 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR36 MUTATED      2    0
  WDR36 WILD-TYPE   64    4
   clus
vv  WDR36 MUTATED WDR36 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D151V7, binary
                 cls
clus               0  1
  WDR36 MUTATED    2  1
  WDR36 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR36 MUTATED      2    1
  WDR36 WILD-TYPE   65   78
        clus
vv       WDR36 MUTATED WDR36 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D151V8, binary
                 cls
clus               0  1
  WDR36 MUTATED    2  1
  WDR36 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR36 MUTATED      2    1
  WDR36 WILD-TYPE   92   35
     clus
vv    WDR36 MUTATED WDR36 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WDR36 MUTATED                                     3
  WDR36 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WDR36 MUTATED                                       0
  WDR36 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WDR36 MUTATED                                                  0
  WDR36 WILD-TYPE                                                2
D151V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D151V10, continuous
[1] "Remove cluster labels:" "WDR36 MUTATED"         
clus
  WDR36 MUTATED WDR36 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-YY-A8LH 
"WDR36 WILD-TYPE" 
D151V11, continuous
[1] "Remove cluster labels:" "WDR36 MUTATED"         
clus
  WDR36 MUTATED WDR36 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  WDR36 MUTATED    2  1  0  0
  WDR36 WILD-TYPE 77 49  4  3
D151V12, multiclass
    clus
vv   WDR36 MUTATED WDR36 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D151V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WDR36 MUTATED       0                         0     2
  WDR36 WILD-TYPE     9                         5   126
D151V14, multiclass
[1] "Remove cluster labels:" "WDR36 MUTATED"         
clus
  WDR36 MUTATED WDR36 WILD-TYPE 
              2             140 
     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-HV-A5A3      TCGA-HV-A5A4 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HV-A5A5      TCGA-HV-A5A6      TCGA-HV-A7OL      TCGA-HV-AA8V 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HV-AA8X      TCGA-HZ-7919      TCGA-HZ-7922      TCGA-HZ-7926 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-8001      TCGA-HZ-8002      TCGA-HZ-8003      TCGA-HZ-8005 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-8315      TCGA-HZ-8317      TCGA-HZ-8519      TCGA-HZ-8636 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-8637      TCGA-HZ-A49G      TCGA-HZ-A49H      TCGA-HZ-A49I 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-A4BH      TCGA-HZ-A4BK      TCGA-HZ-A77O      TCGA-HZ-A77P 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-HZ-A9TJ 
"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-XN-A8T3      TCGA-XN-A8T5 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
     TCGA-YB-A89D      TCGA-YH-A8SY      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" "WDR36 WILD-TYPE" 
D151V15, binary
                 cls
clus                0   1
  WDR36 MUTATED     0   1
  WDR36 WILD-TYPE   5 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR36 MUTATED      0    1
  WDR36 WILD-TYPE    5  104
                        clus
vv                       WDR36 MUTATED WDR36 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             1             104
[1] 2 2
[1] FALSE

Clustering(152) Variable = DRD1 MUTATION ANALYSIS
D152V1, survival
                sevent
clus2             0  1
  DRD1 MUTATED    1  3
  DRD1 WILD-TYPE 67 73
  DRD1 MUTATED DRD1 WILD-TYPE 
             4            140 
  DRD1 MUTATED DRD1 WILD-TYPE 
             3             73 
$`DRD1 MUTATED`
TCGA-3A-A9I9 TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7885 
       20.84        20.19        19.82        41.33 

$`DRD1 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        42.31        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        58.98        43.50         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7926 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  DRD1 MUTATED DRD1 WILD-TYPE 
         19.82           0.03 
  DRD1 MUTATED DRD1 WILD-TYPE 
         41.33          75.12 
  DRD1 MUTATED DRD1 WILD-TYPE 
        20.515         13.990 
[1] "19.8 - 41.3 (20.5)" "0.0 - 75.1 (14.0)" 
[1] "hr=" "1.2"
D152V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DRD1 MUTATED          0        0         1         3         0        0
  DRD1 WILD-TYPE        3        8        22       100         4        4
D152V3, multiclass
           clus
vv          DRD1 MUTATED DRD1 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            1             22
  STAGE IIB            3            100
  STAGE III            0              4
  STAGE IV             0              4
[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
  DRD1 MUTATED     0   0     4
  DRD1 WILD-TYPE   4  16   121
D152V4, multiclass
       clus
vv      DRD1 MUTATED DRD1 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D152V5, binary
                cls
clus               0   1
  DRD1 MUTATED     1   3
  DRD1 WILD-TYPE  36 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD1 MUTATED      1    3
  DRD1 WILD-TYPE   36  105
   clus
vv  DRD1 MUTATED DRD1 WILD-TYPE
  0            1             36
  1            3            105
[1] 2 2
[1] FALSE
D152V6, binary
                cls
clus              0  1
  DRD1 MUTATED    2  0
  DRD1 WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD1 MUTATED      2    0
  DRD1 WILD-TYPE   64    4
   clus
vv  DRD1 MUTATED DRD1 WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D152V7, binary
                cls
clus              0  1
  DRD1 MUTATED    2  2
  DRD1 WILD-TYPE 65 77
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD1 MUTATED      2    2
  DRD1 WILD-TYPE   65   77
        clus
vv       DRD1 MUTATED DRD1 WILD-TYPE
  FEMALE            2             65
  MALE              2             77
[1] 2 2
[1] FALSE
D152V8, binary
                cls
clus              0  1
  DRD1 MUTATED    3  1
  DRD1 WILD-TYPE 91 35
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD1 MUTATED      3    1
  DRD1 WILD-TYPE   91   35
     clus
vv    DRD1 MUTATED DRD1 WILD-TYPE
  NO             3             91
  YES            1             35
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DRD1 MUTATED                                     4
  DRD1 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DRD1 MUTATED                                       0
  DRD1 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DRD1 MUTATED                                                  0
  DRD1 WILD-TYPE                                                2
D152V9, multiclass
                                                  clus
vv                                                 DRD1 MUTATED DRD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D152V10, continuous
D152V11, continuous
[1] "Remove cluster labels:" "DRD1 MUTATED"          
clus
  DRD1 MUTATED DRD1 WILD-TYPE 
             2             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7886     TCGA-IB-7891 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"DRD1 WILD-TYPE" "DRD1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  DRD1 MUTATED    4  0  0  0
  DRD1 WILD-TYPE 75 50  4  3
D152V12, multiclass
    clus
vv   DRD1 MUTATED DRD1 WILD-TYPE
  R0            4             75
  R1            0             50
  R2            0              4
  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"
D152V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DRD1 MUTATED       0                         0     4
  DRD1 WILD-TYPE     9                         5   124
D152V14, multiclass
                           clus
vv                          DRD1 MUTATED DRD1 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V15, binary
                cls
clus               0   1
  DRD1 MUTATED     0   4
  DRD1 WILD-TYPE   5 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD1 MUTATED      0    4
  DRD1 WILD-TYPE    5  101
                        clus
vv                       DRD1 MUTATED DRD1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(153) Variable = ENTPD2 MUTATION ANALYSIS
D153V1, survival
                  sevent
clus2               0  1
  ENTPD2 MUTATED    2  2
  ENTPD2 WILD-TYPE 66 74
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               4              140 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
               2               74 
$`ENTPD2 MUTATED`
TCGA-2L-AAQJ TCGA-FB-A4P6 TCGA-FB-A78T TCGA-IB-7651 
       12.95        11.93         0.03        19.82 

$`ENTPD2 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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       12.66        16.37         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
            0.03             0.13 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
           19.82            75.12 
  ENTPD2 MUTATED ENTPD2 WILD-TYPE 
          12.440           14.435 
[1] "0.0 - 19.8 (12.4)" "0.1 - 75.1 (14.4)"
[1] "hr=" "1.5"
D153V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ENTPD2 MUTATED          0        0         0         3         1        0
  ENTPD2 WILD-TYPE        3        8        23       100         3        4
D153V3, multiclass
           clus
vv          ENTPD2 MUTATED ENTPD2 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              1                3
  STAGE IV               0                4
[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
  ENTPD2 MUTATED     0   0     4
  ENTPD2 WILD-TYPE   4  16   121
D153V4, multiclass
       clus
vv      ENTPD2 MUTATED ENTPD2 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D153V5, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     1   3
  ENTPD2 WILD-TYPE  36 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      1    3
  ENTPD2 WILD-TYPE   36  105
   clus
vv  ENTPD2 MUTATED ENTPD2 WILD-TYPE
  0              1               36
  1              3              105
[1] 2 2
[1] FALSE
D153V6, binary
                  cls
clus                0  1
  ENTPD2 MUTATED    2  0
  ENTPD2 WILD-TYPE 64  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      2    0
  ENTPD2 WILD-TYPE   64    4
   clus
vv  ENTPD2 MUTATED ENTPD2 WILD-TYPE
  0              2               64
  1              0                4
[1] 2 2
[1] FALSE
D153V7, binary
                  cls
clus                0  1
  ENTPD2 MUTATED    3  1
  ENTPD2 WILD-TYPE 64 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      3    1
  ENTPD2 WILD-TYPE   64   78
        clus
vv       ENTPD2 MUTATED ENTPD2 WILD-TYPE
  FEMALE              3               64
  MALE                1               78
[1] 2 2
[1] FALSE
D153V8, binary
                  cls
clus                0  1
  ENTPD2 MUTATED    2  1
  ENTPD2 WILD-TYPE 92 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      2    1
  ENTPD2 WILD-TYPE   92   35
     clus
vv    ENTPD2 MUTATED ENTPD2 WILD-TYPE
  NO               2               92
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ENTPD2 MUTATED                                     4
  ENTPD2 WILD-TYPE                                 126
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ENTPD2 MUTATED                                       0
  ENTPD2 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ENTPD2 MUTATED                                                  0
  ENTPD2 WILD-TYPE                                                2
D153V9, multiclass
                                                  clus
vv                                                 ENTPD2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ENTPD2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D153V10, continuous
D153V11, continuous
                  vv
clus               R0 R1 R2 RX
  ENTPD2 MUTATED    2  1  0  0
  ENTPD2 WILD-TYPE 77 49  4  3
D153V12, multiclass
    clus
vv   ENTPD2 MUTATED ENTPD2 WILD-TYPE
  R0              2               77
  R1              1               49
  R2              0                4
  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"
D153V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ENTPD2 MUTATED       0                         0     4
  ENTPD2 WILD-TYPE     9                         5   124
D153V14, multiclass
                           clus
vv                          ENTPD2 MUTATED ENTPD2 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V15, binary
                  cls
clus                 0   1
  ENTPD2 MUTATED     0   3
  ENTPD2 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD2 MUTATED      0    3
  ENTPD2 WILD-TYPE    5  102
                        clus
vv                       ENTPD2 MUTATED ENTPD2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(154) Variable = SRFBP1 MUTATION ANALYSIS
D154V1, survival
                  sevent
clus2               0  1
  SRFBP1 MUTATED    0  3
  SRFBP1 WILD-TYPE 68 73
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3              141 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               3               73 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
            3.62             0.03 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
           19.82            75.12 
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
             4.7             14.4 
[1] "3.6 - 19.8 (4.7)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "3.6"
D154V2, 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        3        8        23       100         4        4
D154V3, multiclass
           clus
vv          SRFBP1 MUTATED SRFBP1 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   122
D154V4, multiclass
       clus
vv      SRFBP1 MUTATED SRFBP1 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D154V5, binary
                  cls
clus                 0   1
  SRFBP1 MUTATED     0   3
  SRFBP1 WILD-TYPE  37 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      0    3
  SRFBP1 WILD-TYPE   37  105
   clus
vv  SRFBP1 MUTATED SRFBP1 WILD-TYPE
  0              0               37
  1              3              105
[1] 2 2
[1] FALSE
D154V6, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    2  0
  SRFBP1 WILD-TYPE 64  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      2    0
  SRFBP1 WILD-TYPE   64    4
   clus
vv  SRFBP1 MUTATED SRFBP1 WILD-TYPE
  0              2               64
  1              0                4
[1] 2 2
[1] FALSE
D154V7, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    2  1
  SRFBP1 WILD-TYPE 65 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      2    1
  SRFBP1 WILD-TYPE   65   78
        clus
vv       SRFBP1 MUTATED SRFBP1 WILD-TYPE
  FEMALE              2               65
  MALE                1               78
[1] 2 2
[1] FALSE
D154V8, binary
                  cls
clus                0  1
  SRFBP1 MUTATED    3  0
  SRFBP1 WILD-TYPE 91 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      3    0
  SRFBP1 WILD-TYPE   91   36
     clus
vv    SRFBP1 MUTATED SRFBP1 WILD-TYPE
  NO               3               91
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SRFBP1 MUTATED                                     3
  SRFBP1 WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SRFBP1 MUTATED                                       0
  SRFBP1 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SRFBP1 MUTATED                                                  0
  SRFBP1 WILD-TYPE                                                2
D154V9, 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                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D154V10, continuous
D154V11, continuous
[1] "Remove cluster labels:" "SRFBP1 MUTATED"        
clus
  SRFBP1 MUTATED SRFBP1 WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" "SRFBP1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  SRFBP1 MUTATED    1  2  0  0
  SRFBP1 WILD-TYPE 78 48  4  3
D154V12, multiclass
    clus
vv   SRFBP1 MUTATED SRFBP1 WILD-TYPE
  R0              1               78
  R1              2               48
  R2              0                4
  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"
D154V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SRFBP1 MUTATED       0                         0     3
  SRFBP1 WILD-TYPE     9                         5   125
D154V14, multiclass
                           clus
vv                          SRFBP1 MUTATED SRFBP1 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V15, binary
                  cls
clus                 0   1
  SRFBP1 MUTATED     0   2
  SRFBP1 WILD-TYPE   5 103
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRFBP1 MUTATED      0    2
  SRFBP1 WILD-TYPE    5  103
                        clus
vv                       SRFBP1 MUTATED SRFBP1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              2              103
[1] 2 2
[1] FALSE

Clustering(155) Variable = CSRNP3 MUTATION ANALYSIS
D155V1, survival
                  sevent
clus2               0  1
  CSRNP3 MUTATED    1  2
  CSRNP3 WILD-TYPE 67 74
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               3              141 
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               2               74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       19.82        12.95         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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
           11.93             0.03 
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
           49.38            75.12 
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
           19.82            14.17 
[1] "11.9 - 49.4 (19.8)" "0.0 - 75.1 (14.2)" 
[1] "hr=" "1.3"
D155V2, 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        3        8        23        99         4        4
D155V3, multiclass
           clus
vv          CSRNP3 MUTATED CSRNP3 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              4               99
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   121
D155V4, multiclass
       clus
vv      CSRNP3 MUTATED CSRNP3 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D155V5, binary
                  cls
clus                 0   1
  CSRNP3 MUTATED     0   4
  CSRNP3 WILD-TYPE  37 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSRNP3 MUTATED      0    4
  CSRNP3 WILD-TYPE   37  104
   clus
vv  CSRNP3 MUTATED CSRNP3 WILD-TYPE
  0              0               37
  1              4              104
[1] 2 2
[1] FALSE
D155V6, binary
                  cls
clus                0  1
  CSRNP3 MUTATED    2  0
  CSRNP3 WILD-TYPE 64  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSRNP3 MUTATED      2    0
  CSRNP3 WILD-TYPE   64    4
   clus
vv  CSRNP3 MUTATED CSRNP3 WILD-TYPE
  0              2               64
  1              0                4
[1] 2 2
[1] FALSE
D155V7, binary
                  cls
clus                0  1
  CSRNP3 MUTATED    3  1
  CSRNP3 WILD-TYPE 64 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSRNP3 MUTATED      3    1
  CSRNP3 WILD-TYPE   64   78
        clus
vv       CSRNP3 MUTATED CSRNP3 WILD-TYPE
  FEMALE              3               64
  MALE                1               78
[1] 2 2
[1] FALSE
D155V8, binary
                  cls
clus                0  1
  CSRNP3 MUTATED    2  1
  CSRNP3 WILD-TYPE 92 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSRNP3 MUTATED      2    1
  CSRNP3 WILD-TYPE   92   35
     clus
vv    CSRNP3 MUTATED CSRNP3 WILD-TYPE
  NO               2               92
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CSRNP3 MUTATED                                     4
  CSRNP3 WILD-TYPE                                 126
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CSRNP3 MUTATED                                       0
  CSRNP3 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CSRNP3 MUTATED                                                  0
  CSRNP3 WILD-TYPE                                                2
D155V9, 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                           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D155V10, continuous
[1] "Remove cluster labels:" "CSRNP3 MUTATED"        
clus
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               2               48 
      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-HV-AA8V 
"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-7887 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
D155V11, continuous
[1] "Remove cluster labels:" "CSRNP3 MUTATED"        
clus
  CSRNP3 MUTATED CSRNP3 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"CSRNP3 WILD-TYPE" "CSRNP3 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CSRNP3 MUTATED    3  0  0  0
  CSRNP3 WILD-TYPE 76 50  4  3
D155V12, multiclass
    clus
vv   CSRNP3 MUTATED CSRNP3 WILD-TYPE
  R0              3               76
  R1              0               50
  R2              0                4
  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"
D155V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSRNP3 MUTATED       0                         0     3
  CSRNP3 WILD-TYPE     9                         5   125
D155V14, multiclass
                           clus
vv                          CSRNP3 MUTATED CSRNP3 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V15, binary
                  cls
clus                 0   1
  CSRNP3 MUTATED     1   2
  CSRNP3 WILD-TYPE   4 103
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSRNP3 MUTATED      1    2
  CSRNP3 WILD-TYPE    4  103
                        clus
vv                       CSRNP3 MUTATED CSRNP3 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO              2              103
[1] 2 2
[1] FALSE

Clustering(156) Variable = REXO1 MUTATION ANALYSIS
D156V1, survival
                 sevent
clus2              0  1
  REXO1 MUTATED    0  3
  REXO1 WILD-TYPE 68 73
  REXO1 MUTATED REXO1 WILD-TYPE 
              3             141 
  REXO1 MUTATED REXO1 WILD-TYPE 
              3              73 
$`REXO1 MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7887 
       20.19        19.82         3.62 

$`REXO1 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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  REXO1 MUTATED REXO1 WILD-TYPE 
           3.62            0.03 
  REXO1 MUTATED REXO1 WILD-TYPE 
          20.19           75.12 
  REXO1 MUTATED REXO1 WILD-TYPE 
          19.82           14.17 
[1] "3.6 - 20.2 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "2"  
D156V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  REXO1 MUTATED          0        0         0         3         0        0
  REXO1 WILD-TYPE        3        8        23       100         4        4
D156V3, multiclass
           clus
vv          REXO1 MUTATED REXO1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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
  REXO1 MUTATED     0   0     3
  REXO1 WILD-TYPE   4  16   122
D156V4, multiclass
       clus
vv      REXO1 MUTATED REXO1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D156V5, binary
                 cls
clus                0   1
  REXO1 MUTATED     0   3
  REXO1 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO1 MUTATED      0    3
  REXO1 WILD-TYPE   37  105
   clus
vv  REXO1 MUTATED REXO1 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D156V6, binary
                 cls
clus               0  1
  REXO1 MUTATED    2  0
  REXO1 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO1 MUTATED      2    0
  REXO1 WILD-TYPE   64    4
   clus
vv  REXO1 MUTATED REXO1 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D156V7, binary
                 cls
clus               0  1
  REXO1 MUTATED    2  1
  REXO1 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO1 MUTATED      2    1
  REXO1 WILD-TYPE   65   78
        clus
vv       REXO1 MUTATED REXO1 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D156V8, binary
                 cls
clus               0  1
  REXO1 MUTATED    3  0
  REXO1 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO1 MUTATED      3    0
  REXO1 WILD-TYPE   91   36
     clus
vv    REXO1 MUTATED REXO1 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  REXO1 MUTATED                                     3
  REXO1 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  REXO1 MUTATED                                       0
  REXO1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  REXO1 MUTATED                                                  0
  REXO1 WILD-TYPE                                                2
D156V9, multiclass
                                                  clus
vv                                                 REXO1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 REXO1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D156V10, continuous
[1] "Remove cluster labels:" "REXO1 MUTATED"         
clus
  REXO1 MUTATED REXO1 WILD-TYPE 
              2              48 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
D156V11, continuous
[1] "Remove cluster labels:" "REXO1 MUTATED"         
clus
  REXO1 MUTATED REXO1 WILD-TYPE 
              1              39 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7885      TCGA-IB-7886 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"REXO1 WILD-TYPE" "REXO1 WILD-TYPE" "REXO1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  REXO1 MUTATED    2  1  0  0
  REXO1 WILD-TYPE 77 49  4  3
D156V12, multiclass
    clus
vv   REXO1 MUTATED REXO1 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D156V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  REXO1 MUTATED       0                         0     3
  REXO1 WILD-TYPE     9                         5   125
D156V14, multiclass
                           clus
vv                          REXO1 MUTATED REXO1 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V15, binary
                 cls
clus                0   1
  REXO1 MUTATED     0   3
  REXO1 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO1 MUTATED      0    3
  REXO1 WILD-TYPE    5  102
                        clus
vv                       REXO1 MUTATED REXO1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(157) Variable = CEACAM4 MUTATION ANALYSIS
D157V1, survival
                   sevent
clus2                0  1
  CEACAM4 MUTATED    1  3
  CEACAM4 WILD-TYPE 67 73
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                4               140 
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                3                73 
$`CEACAM4 MUTATED`
TCGA-2J-AAB6 TCGA-FB-AAQ2 TCGA-HV-A7OL TCGA-IB-7651 
        9.63         5.03         8.28        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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-AA8V 
       13.84         4.21         7.63         9.50        66.94        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
             5.03              0.03 
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
            19.82             75.12 
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
            8.955            14.435 
[1] "5.0 - 19.8 (9.0)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "2.4"
D157V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CEACAM4 MUTATED          0        0         2         2         0        0
  CEACAM4 WILD-TYPE        3        8        21       101         4        4
D157V3, multiclass
           clus
vv          CEACAM4 MUTATED CEACAM4 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               2                21
  STAGE IIB               2               101
  STAGE III               0                 4
  STAGE IV                0                 4
[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     4
  CEACAM4 WILD-TYPE   4  16   121
D157V4, multiclass
       clus
vv      CEACAM4 MUTATED CEACAM4 WILD-TYPE
  T1                  0                 4
  T2                  0                16
  T3+T4               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"
D157V5, binary
                   cls
clus                  0   1
  CEACAM4 MUTATED     2   2
  CEACAM4 WILD-TYPE  35 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM4 MUTATED      2    2
  CEACAM4 WILD-TYPE   35  106
   clus
vv  CEACAM4 MUTATED CEACAM4 WILD-TYPE
  0               2                35
  1               2               106
[1] 2 2
[1] FALSE
D157V6, binary
                   cls
clus                 0  1
  CEACAM4 MUTATED    2  0
  CEACAM4 WILD-TYPE 64  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM4 MUTATED      2    0
  CEACAM4 WILD-TYPE   64    4
   clus
vv  CEACAM4 MUTATED CEACAM4 WILD-TYPE
  0               2                64
  1               0                 4
[1] 2 2
[1] FALSE
D157V7, binary
                   cls
clus                 0  1
  CEACAM4 MUTATED    2  2
  CEACAM4 WILD-TYPE 65 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM4 MUTATED      2    2
  CEACAM4 WILD-TYPE   65   77
        clus
vv       CEACAM4 MUTATED CEACAM4 WILD-TYPE
  FEMALE               2                65
  MALE                 2                77
[1] 2 2
[1] FALSE
D157V8, binary
                   cls
clus                 0  1
  CEACAM4 MUTATED    4  0
  CEACAM4 WILD-TYPE 90 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM4 MUTATED      4    0
  CEACAM4 WILD-TYPE   90   36
     clus
vv    CEACAM4 MUTATED CEACAM4 WILD-TYPE
  NO                4                90
  YES               0                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CEACAM4 MUTATED                                     4
  CEACAM4 WILD-TYPE                                 126
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CEACAM4 MUTATED                                       0
  CEACAM4 WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CEACAM4 MUTATED                                                  0
  CEACAM4 WILD-TYPE                                                2
D157V9, multiclass
                                                  clus
vv                                                 CEACAM4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 CEACAM4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D157V10, continuous
[1] "Remove cluster labels:" "CEACAM4 MUTATED"       
clus
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                1                49 
       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-HV-AA8V        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-7887        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-8127 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-IB-AAUQ        TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-S4-A8RP        TCGA-US-A774        TCGA-XD-AAUL        TCGA-XN-A8T5 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
       TCGA-YY-A8LH 
"CEACAM4 WILD-TYPE" 
D157V11, continuous
[1] "Remove cluster labels:" "CEACAM4 MUTATED"       
clus
  CEACAM4 MUTATED CEACAM4 WILD-TYPE 
                1                39 
       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-XN-A8T5        TCGA-YY-A8LH 
"CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" "CEACAM4 WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  CEACAM4 MUTATED    2  1  1  0
  CEACAM4 WILD-TYPE 77 49  3  3
D157V12, multiclass
    clus
vv   CEACAM4 MUTATED CEACAM4 WILD-TYPE
  R0               2                77
  R1               1                49
  R2               1                 3
  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"
D157V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEACAM4 MUTATED       1                         0     3
  CEACAM4 WILD-TYPE     8                         5   125
D157V14, multiclass
                           clus
vv                          CEACAM4 MUTATED CEACAM4 WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   3               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V15, binary
                   cls
clus                  0   1
  CEACAM4 MUTATED     0   2
  CEACAM4 WILD-TYPE   5 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM4 MUTATED      0    2
  CEACAM4 WILD-TYPE    5  103
                        clus
vv                       CEACAM4 MUTATED CEACAM4 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2               103
[1] 2 2
[1] FALSE

Clustering(158) Variable = SARS2 MUTATION ANALYSIS
D158V1, survival
                 sevent
clus2              0  1
  SARS2 MUTATED    1  2
  SARS2 WILD-TYPE 67 74
  SARS2 MUTATED SARS2 WILD-TYPE 
              3             141 
  SARS2 MUTATED SARS2 WILD-TYPE 
              2              74 
$`SARS2 MUTATED`
TCGA-2J-AAB1 TCGA-FB-A78T TCGA-RB-A7B8 
        2.17         0.03        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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       13.68         3.12         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  SARS2 MUTATED SARS2 WILD-TYPE 
           0.03            0.13 
  SARS2 MUTATED SARS2 WILD-TYPE 
          15.32           75.12 
  SARS2 MUTATED SARS2 WILD-TYPE 
           2.17           14.40 
[1] "0.0 - 15.3 (2.2)"  "0.1 - 75.1 (14.4)"
[1] "hr=" "4.3"
D158V2, 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        3        8        23       100         4        4
D158V3, multiclass
           clus
vv          SARS2 MUTATED SARS2 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D158V4, multiclass
       clus
vv      SARS2 MUTATED SARS2 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D158V5, binary
                 cls
clus                0   1
  SARS2 MUTATED     0   3
  SARS2 WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      0    3
  SARS2 WILD-TYPE   37  105
   clus
vv  SARS2 MUTATED SARS2 WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D158V6, binary
                 cls
clus               0  1
  SARS2 MUTATED    2  0
  SARS2 WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      2    0
  SARS2 WILD-TYPE   64    4
   clus
vv  SARS2 MUTATED SARS2 WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D158V7, binary
                 cls
clus               0  1
  SARS2 MUTATED    2  1
  SARS2 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      2    1
  SARS2 WILD-TYPE   65   78
        clus
vv       SARS2 MUTATED SARS2 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D158V8, binary
                 cls
clus               0  1
  SARS2 MUTATED    2  0
  SARS2 WILD-TYPE 92 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      2    0
  SARS2 WILD-TYPE   92   36
     clus
vv    SARS2 MUTATED SARS2 WILD-TYPE
  NO              2              92
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SARS2 MUTATED                                     1
  SARS2 WILD-TYPE                                 129
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SARS2 MUTATED                                       2
  SARS2 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SARS2 MUTATED                                                  0
  SARS2 WILD-TYPE                                                2
D158V9, 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                          129
  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"
D158V10, continuous
[1] "Remove cluster labels:" "SARS2 MUTATED"         
clus
  SARS2 MUTATED SARS2 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
D158V11, continuous
[1] "Remove cluster labels:" "SARS2 MUTATED"         
clus
  SARS2 MUTATED SARS2 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"SARS2 WILD-TYPE" "SARS2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  SARS2 MUTATED    3  0  0  0
  SARS2 WILD-TYPE 76 50  4  3
D158V12, multiclass
    clus
vv   SARS2 MUTATED SARS2 WILD-TYPE
  R0             3              76
  R1             0              50
  R2             0               4
  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"
D158V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SARS2 MUTATED       0                         0     3
  SARS2 WILD-TYPE     9                         5   125
D158V14, multiclass
                           clus
vv                          SARS2 MUTATED SARS2 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V15, binary
                 cls
clus                0   1
  SARS2 MUTATED     0   2
  SARS2 WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SARS2 MUTATED      0    2
  SARS2 WILD-TYPE    5  103
                        clus
vv                       SARS2 MUTATED SARS2 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(159) Variable = CPNE2 MUTATION ANALYSIS
D159V1, survival
                 sevent
clus2              0  1
  CPNE2 MUTATED    1  2
  CPNE2 WILD-TYPE 67 74
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              3             141 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2              74 
$`CPNE2 MUTATED`
TCGA-3A-A9I5 TCGA-3E-AAAZ TCGA-IB-7651 
       58.98        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        42.31        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        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  CPNE2 MUTATED CPNE2 WILD-TYPE 
          19.82            0.03 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
          71.74           75.12 
  CPNE2 MUTATED CPNE2 WILD-TYPE 
          58.98           14.14 
[1] "19.8 - 71.7 (59.0)" "0.0 - 75.1 (14.1)" 
[1] "hr=" "2.5"
D159V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CPNE2 MUTATED          0        0         1         1         0        0
  CPNE2 WILD-TYPE        3        8        22       102         4        4
D159V3, multiclass
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2             143 
     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-3E-AAAY      TCGA-F2-6879      TCGA-F2-A44G      TCGA-F2-A44H 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A4P5      TCGA-FB-A4P6 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-A545      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPU      TCGA-FB-AAPY      TCGA-FB-AAPZ      TCGA-FB-AAQ0 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-H6-8124 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-H6-A45N      TCGA-HV-A5A3      TCGA-HV-A5A4      TCGA-HV-A5A5 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HV-A5A6      TCGA-HV-A7OL      TCGA-HV-AA8V      TCGA-HV-AA8X 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-7919      TCGA-HZ-7922      TCGA-HZ-7925      TCGA-HZ-7926 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-8001      TCGA-HZ-8002      TCGA-HZ-8003      TCGA-HZ-8005 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-8315      TCGA-HZ-8317      TCGA-HZ-8519      TCGA-HZ-8636 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-8637      TCGA-HZ-A49G      TCGA-HZ-A49H      TCGA-HZ-A49I 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A4BH      TCGA-HZ-A4BK      TCGA-HZ-A77O      TCGA-HZ-A77P 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-HZ-A9TJ 
"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-PZ-A5RE      TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-RB-AA9M      TCGA-S4-A8RM      TCGA-S4-A8RO      TCGA-S4-A8RP 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A774      TCGA-US-A776      TCGA-US-A779      TCGA-US-A77E 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A77G      TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-YH-A8SY      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
                 vv
clus               T1  T2 T3+T4
  CPNE2 MUTATED     0   0     2
  CPNE2 WILD-TYPE   4  16   123
D159V4, multiclass
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2             143 
     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-3E-AAAY      TCGA-F2-6879      TCGA-F2-A44G      TCGA-F2-A44H 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-F2-A7TX      TCGA-F2-A8YN      TCGA-FB-A4P5      TCGA-FB-A4P6 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-A545      TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAPU      TCGA-FB-AAPY      TCGA-FB-AAPZ      TCGA-FB-AAQ0 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-FB-AAQ1      TCGA-FB-AAQ2      TCGA-FB-AAQ3      TCGA-H6-8124 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-H6-A45N      TCGA-HV-A5A3      TCGA-HV-A5A4      TCGA-HV-A5A5 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HV-A5A6      TCGA-HV-A7OL      TCGA-HV-AA8V      TCGA-HV-AA8X 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-7919      TCGA-HZ-7922      TCGA-HZ-7925      TCGA-HZ-7926 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-8001      TCGA-HZ-8002      TCGA-HZ-8003      TCGA-HZ-8005 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-8315      TCGA-HZ-8317      TCGA-HZ-8519      TCGA-HZ-8636 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-8637      TCGA-HZ-A49G      TCGA-HZ-A49H      TCGA-HZ-A49I 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A4BH      TCGA-HZ-A4BK      TCGA-HZ-A77O      TCGA-HZ-A77P 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1      TCGA-HZ-A9TJ 
"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-PZ-A5RE      TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-RB-AA9M      TCGA-S4-A8RM      TCGA-S4-A8RO      TCGA-S4-A8RP 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A774      TCGA-US-A776      TCGA-US-A779      TCGA-US-A77E 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A77G      TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-YH-A8SY      TCGA-YY-A8LH      TCGA-Z5-AAPL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
D159V5, binary
                 cls
clus                0   1
  CPNE2 MUTATED     2   1
  CPNE2 WILD-TYPE  35 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      2    1
  CPNE2 WILD-TYPE   35  107
   clus
vv  CPNE2 MUTATED CPNE2 WILD-TYPE
  0             2              35
  1             1             107
[1] 2 2
[1] FALSE
D159V6, binary
                 cls
clus               0  1
  CPNE2 MUTATED    1  0
  CPNE2 WILD-TYPE 65  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    0
  CPNE2 WILD-TYPE   65    4
   clus
vv  CPNE2 MUTATED CPNE2 WILD-TYPE
  0             1              65
  1             0               4
[1] 2 2
[1] FALSE
D159V7, binary
                 cls
clus               0  1
  CPNE2 MUTATED    1  2
  CPNE2 WILD-TYPE 66 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    2
  CPNE2 WILD-TYPE   66   77
        clus
vv       CPNE2 MUTATED CPNE2 WILD-TYPE
  FEMALE             1              66
  MALE               2              77
[1] 2 2
[1] FALSE
D159V8, binary
                 cls
clus               0  1
  CPNE2 MUTATED    1  1
  CPNE2 WILD-TYPE 93 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    1
  CPNE2 WILD-TYPE   93   35
     clus
vv    CPNE2 MUTATED CPNE2 WILD-TYPE
  NO              1              93
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CPNE2 MUTATED                                     3
  CPNE2 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CPNE2 MUTATED                                       0
  CPNE2 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CPNE2 MUTATED                                                  0
  CPNE2 WILD-TYPE                                                2
D159V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D159V10, continuous
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-YY-A8LH 
"CPNE2 WILD-TYPE" 
D159V11, continuous
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CPNE2 MUTATED    2  0  0  0
  CPNE2 WILD-TYPE 77 50  4  3
D159V12, multiclass
[1] "Remove cluster labels:" "CPNE2 MUTATED"         
clus
  CPNE2 MUTATED CPNE2 WILD-TYPE 
              2             134 
     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-HV-A5A6      TCGA-HV-A7OL      TCGA-HV-AA8V 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-HV-AA8X      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-HZ-A9TJ      TCGA-IB-7644      TCGA-IB-7645      TCGA-IB-7646 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7647      TCGA-IB-7649      TCGA-IB-7652      TCGA-IB-7885 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7888      TCGA-IB-7889 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-7890      TCGA-IB-7891      TCGA-IB-7893      TCGA-IB-7897 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SO      TCGA-IB-A5SP 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A5SQ      TCGA-IB-A5SS      TCGA-IB-A5ST      TCGA-IB-A6UF 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7LX      TCGA-IB-A7M4      TCGA-IB-AAUM 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUN      TCGA-IB-AAUO      TCGA-IB-AAUP      TCGA-IB-AAUQ 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-IB-AAUR      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A8F3      TCGA-LB-A9Q5      TCGA-M8-A5N4 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-OE-A75W      TCGA-Q3-A5QY      TCGA-Q3-AA2A      TCGA-RB-A7B8 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-RB-AA9M      TCGA-S4-A8RM      TCGA-S4-A8RO      TCGA-S4-A8RP 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A774      TCGA-US-A776      TCGA-US-A779      TCGA-US-A77E 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-US-A77G      TCGA-XD-AAUG      TCGA-XD-AAUH      TCGA-XD-AAUI 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-XD-AAUL      TCGA-XN-A8T3      TCGA-XN-A8T5      TCGA-YB-A89D 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
     TCGA-YY-A8LH      TCGA-Z5-AAPL 
"CPNE2 WILD-TYPE" "CPNE2 WILD-TYPE" 
D159V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CPNE2 MUTATED       0                         0     3
  CPNE2 WILD-TYPE     9                         5   125
D159V14, multiclass
                           clus
vv                          CPNE2 MUTATED CPNE2 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V15, binary
                 cls
clus                0   1
  CPNE2 MUTATED     1   2
  CPNE2 WILD-TYPE   4 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPNE2 MUTATED      1    2
  CPNE2 WILD-TYPE    4  103
                        clus
vv                       CPNE2 MUTATED CPNE2 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(160) Variable = CYTSA MUTATION ANALYSIS
D160V1, survival
                 sevent
clus2              0  1
  CYTSA MUTATED    1  3
  CYTSA WILD-TYPE 67 73
  CYTSA MUTATED CYTSA WILD-TYPE 
              4             140 
  CYTSA MUTATED CYTSA WILD-TYPE 
              3              73 
$`CYTSA MUTATED`
TCGA-HV-A5A3 TCGA-HZ-7926 TCGA-IB-7651 TCGA-IB-7885 
        4.21        17.03        19.82        41.33 

$`CYTSA 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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
        1.02        12.89        13.84         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  CYTSA MUTATED CYTSA WILD-TYPE 
           4.21            0.03 
  CYTSA MUTATED CYTSA WILD-TYPE 
          41.33           75.12 
  CYTSA MUTATED CYTSA WILD-TYPE 
         18.425          14.155 
[1] "4.2 - 41.3 (18.4)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.2"
D160V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CYTSA MUTATED          0        0         1         3         0        0
  CYTSA WILD-TYPE        3        8        22       100         4        4
D160V3, multiclass
           clus
vv          CYTSA MUTATED CYTSA WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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
  CYTSA MUTATED     0   0     4
  CYTSA WILD-TYPE   4  16   121
D160V4, multiclass
       clus
vv      CYTSA MUTATED CYTSA WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D160V5, binary
                 cls
clus                0   1
  CYTSA MUTATED     0   3
  CYTSA WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTSA MUTATED      0    3
  CYTSA WILD-TYPE   37  105
   clus
vv  CYTSA MUTATED CYTSA WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D160V6, binary
                 cls
clus               0  1
  CYTSA MUTATED    2  0
  CYTSA WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTSA MUTATED      2    0
  CYTSA WILD-TYPE   64    4
   clus
vv  CYTSA MUTATED CYTSA WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D160V7, binary
                 cls
clus               0  1
  CYTSA MUTATED    2  2
  CYTSA WILD-TYPE 65 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTSA MUTATED      2    2
  CYTSA WILD-TYPE   65   77
        clus
vv       CYTSA MUTATED CYTSA WILD-TYPE
  FEMALE             2              65
  MALE               2              77
[1] 2 2
[1] FALSE
D160V8, binary
                 cls
clus               0  1
  CYTSA MUTATED    3  0
  CYTSA WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTSA MUTATED      3    0
  CYTSA WILD-TYPE   91   36
     clus
vv    CYTSA MUTATED CYTSA WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CYTSA MUTATED                                     4
  CYTSA WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CYTSA MUTATED                                       0
  CYTSA WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CYTSA MUTATED                                                  0
  CYTSA WILD-TYPE                                                2
D160V9, multiclass
                                                  clus
vv                                                 CYTSA MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CYTSA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D160V10, continuous
[1] "Remove cluster labels:" "CYTSA MUTATED"         
clus
  CYTSA MUTATED CYTSA WILD-TYPE 
              2              48 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7886      TCGA-IB-7887 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
D160V11, continuous
[1] "Remove cluster labels:" "CYTSA MUTATED"         
clus
  CYTSA MUTATED CYTSA WILD-TYPE 
              2              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7886      TCGA-IB-7891 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UF 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ      TCGA-IB-AAUS 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"CYTSA WILD-TYPE" "CYTSA WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  CYTSA MUTATED    2  0  0  1
  CYTSA WILD-TYPE 77 50  4  2
D160V12, multiclass
    clus
vv   CYTSA MUTATED CYTSA WILD-TYPE
  R0             2              77
  R1             0              50
  R2             0               4
  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"
D160V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYTSA MUTATED       1                         1     2
  CYTSA WILD-TYPE     8                         4   126
D160V14, multiclass
                           clus
vv                          CYTSA MUTATED CYTSA WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             1               4
  WHITE                                 2             126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V15, binary
                 cls
clus                0   1
  CYTSA MUTATED     0   3
  CYTSA WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYTSA MUTATED      0    3
  CYTSA WILD-TYPE    5  102
                        clus
vv                       CYTSA MUTATED CYTSA WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(161) Variable = LUZP1 MUTATION ANALYSIS
D161V1, survival
                 sevent
clus2              0  1
  LUZP1 MUTATED    2  2
  LUZP1 WILD-TYPE 66 74
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              4             140 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              2              74 
$`LUZP1 MUTATED`
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-IB-A6UF TCGA-OE-A75W 
       66.94         8.28        21.90         8.78 

$`LUZP1 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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  LUZP1 MUTATED LUZP1 WILD-TYPE 
           8.28            0.03 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
          66.94           75.12 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
         15.340          14.285 
[1] "8.3 - 66.9 (15.3)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.6"
D161V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  LUZP1 MUTATED          0        0         2         2         0        0
  LUZP1 WILD-TYPE        3        8        21       101         4        4
D161V3, multiclass
           clus
vv          LUZP1 MUTATED LUZP1 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             2              21
  STAGE IIB             2             101
  STAGE III             0               4
  STAGE IV              0               4
[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
  LUZP1 MUTATED     0   0     4
  LUZP1 WILD-TYPE   4  16   121
D161V4, multiclass
       clus
vv      LUZP1 MUTATED LUZP1 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D161V5, binary
                 cls
clus                0   1
  LUZP1 MUTATED     2   2
  LUZP1 WILD-TYPE  35 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      2    2
  LUZP1 WILD-TYPE   35  106
   clus
vv  LUZP1 MUTATED LUZP1 WILD-TYPE
  0             2              35
  1             2             106
[1] 2 2
[1] FALSE
D161V6, binary
                 cls
clus               0  1
  LUZP1 MUTATED    3  0
  LUZP1 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      3    0
  LUZP1 WILD-TYPE   63    4
   clus
vv  LUZP1 MUTATED LUZP1 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D161V7, binary
                 cls
clus               0  1
  LUZP1 MUTATED    1  3
  LUZP1 WILD-TYPE 66 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      1    3
  LUZP1 WILD-TYPE   66   76
        clus
vv       LUZP1 MUTATED LUZP1 WILD-TYPE
  FEMALE             1              66
  MALE               3              76
[1] 2 2
[1] FALSE
D161V8, binary
                 cls
clus               0  1
  LUZP1 MUTATED    3  1
  LUZP1 WILD-TYPE 91 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      3    1
  LUZP1 WILD-TYPE   91   35
     clus
vv    LUZP1 MUTATED LUZP1 WILD-TYPE
  NO              3              91
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LUZP1 MUTATED                                     4
  LUZP1 WILD-TYPE                                 126
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LUZP1 MUTATED                                       0
  LUZP1 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LUZP1 MUTATED                                                  0
  LUZP1 WILD-TYPE                                                2
D161V9, multiclass
                                                  clus
vv                                                 LUZP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 LUZP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D161V10, continuous
[1] "Remove cluster labels:" "LUZP1 MUTATED"         
clus
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              2              48 
     TCGA-2J-AAB1      TCGA-2J-AABA      TCGA-2J-AABE      TCGA-2J-AABF 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-2J-AABO      TCGA-2J-AABV      TCGA-2L-AAQA      TCGA-2L-AAQE 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-3A-A9I9      TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-F2-A8YN 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FB-A4P5      TCGA-FB-A4P6      TCGA-FB-A5VM      TCGA-FB-A78T 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FB-AAPS      TCGA-FB-AAPY      TCGA-H6-8124      TCGA-H6-A45N 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-HV-AA8V      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7887      TCGA-IB-7891      TCGA-IB-8126 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-8127      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-IB-A7M4 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-S4-A8RM      TCGA-S4-A8RP 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
D161V11, continuous
[1] "Remove cluster labels:" "LUZP1 MUTATED"         
clus
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              2              38 
     TCGA-2J-AAB1      TCGA-2J-AABE      TCGA-2J-AABF      TCGA-2J-AABO 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-3A-A9IB      TCGA-3A-A9IX      TCGA-FB-A4P5      TCGA-FB-A4P6 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-AAPS      TCGA-FB-AAPY 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-H6-8124      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-LB-A7SX      TCGA-LB-A9Q5 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-S4-A8RM      TCGA-US-A774      TCGA-XD-AAUI      TCGA-XD-AAUL 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
     TCGA-XN-A8T5      TCGA-YY-A8LH 
"LUZP1 WILD-TYPE" "LUZP1 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  LUZP1 MUTATED    2  1  1  0
  LUZP1 WILD-TYPE 77 49  3  3
D161V12, multiclass
    clus
vv   LUZP1 MUTATED LUZP1 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             1               3
  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"
D161V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LUZP1 MUTATED       2                         0     2
  LUZP1 WILD-TYPE     7                         5   126
D161V14, multiclass
                           clus
vv                          LUZP1 MUTATED LUZP1 WILD-TYPE
  ASIAN                                 2               7
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 2             126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V15, binary
                 cls
clus                0   1
  LUZP1 MUTATED     0   2
  LUZP1 WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      0    2
  LUZP1 WILD-TYPE    5  103
                        clus
vv                       LUZP1 MUTATED LUZP1 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(162) Variable = CCDC87 MUTATION ANALYSIS
D162V1, survival
                  sevent
clus2               0  1
  CCDC87 MUTATED    2  1
  CCDC87 WILD-TYPE 66 75
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               3              141 
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               1               75 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       19.82        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-AAUM TCGA-IB-AAUN TCGA-IB-AAUO 
       21.90         1.35         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-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
       13.68        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  CCDC87 MUTATED CCDC87 WILD-TYPE 
            3.12             0.03 
  CCDC87 MUTATED CCDC87 WILD-TYPE 
           15.88            75.12 
  CCDC87 MUTATED CCDC87 WILD-TYPE 
            5.88            14.40 
[1] "3.1 - 15.9 (5.9)"  "0.0 - 75.1 (14.4)"
[1] "hr=" "1.5"
D162V2, 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        3        7        23       101         4        4
D162V3, multiclass
           clus
vv          CCDC87 MUTATED CCDC87 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               1                7
  STAGE IIA              0               23
  STAGE IIB              2              101
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   122
D162V4, multiclass
       clus
vv      CCDC87 MUTATED CCDC87 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D162V5, binary
                  cls
clus                 0   1
  CCDC87 MUTATED     0   3
  CCDC87 WILD-TYPE  37 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC87 MUTATED      0    3
  CCDC87 WILD-TYPE   37  105
   clus
vv  CCDC87 MUTATED CCDC87 WILD-TYPE
  0              0               37
  1              3              105
[1] 2 2
[1] FALSE
D162V6, binary
                  cls
clus                0  1
  CCDC87 MUTATED    0  0
  CCDC87 WILD-TYPE 66  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC87 MUTATED      0    0
  CCDC87 WILD-TYPE   66    4
D162V7, binary
                  cls
clus                0  1
  CCDC87 MUTATED    2  1
  CCDC87 WILD-TYPE 65 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC87 MUTATED      2    1
  CCDC87 WILD-TYPE   65   78
        clus
vv       CCDC87 MUTATED CCDC87 WILD-TYPE
  FEMALE              2               65
  MALE                1               78
[1] 2 2
[1] FALSE
D162V8, binary
                  cls
clus                0  1
  CCDC87 MUTATED    2  0
  CCDC87 WILD-TYPE 92 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC87 MUTATED      2    0
  CCDC87 WILD-TYPE   92   36
     clus
vv    CCDC87 MUTATED CCDC87 WILD-TYPE
  NO               2               92
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC87 MUTATED                                     3
  CCDC87 WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC87 MUTATED                                       0
  CCDC87 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC87 MUTATED                                                  0
  CCDC87 WILD-TYPE                                                2
D162V9, 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                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D162V10, continuous
[1] "Remove cluster labels:" "CCDC87 MUTATED"        
clus
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               2               48 
      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-HV-AA8V 
"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-7887       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-A5SS       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-AAUQ 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
D162V11, continuous
[1] "Remove cluster labels:" "CCDC87 MUTATED"        
clus
  CCDC87 MUTATED CCDC87 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"CCDC87 WILD-TYPE" "CCDC87 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  CCDC87 MUTATED    2  0  0  1
  CCDC87 WILD-TYPE 77 50  4  2
D162V12, multiclass
    clus
vv   CCDC87 MUTATED CCDC87 WILD-TYPE
  R0              2               77
  R1              0               50
  R2              0                4
  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"
D162V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC87 MUTATED       0                         0     3
  CCDC87 WILD-TYPE     9                         5   125
D162V14, multiclass
                           clus
vv                          CCDC87 MUTATED CCDC87 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V15, binary
                  cls
clus                 0   1
  CCDC87 MUTATED     0   3
  CCDC87 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC87 MUTATED      0    3
  CCDC87 WILD-TYPE    5  102
                        clus
vv                       CCDC87 MUTATED CCDC87 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(163) Variable = ZBTB4 MUTATION ANALYSIS
D163V1, survival
                 sevent
clus2              0  1
  ZBTB4 MUTATED    0  4
  ZBTB4 WILD-TYPE 68 72
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              4             140 
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              4              72 
$`ZBTB4 MUTATED`
TCGA-HV-A5A6 TCGA-HZ-8636 TCGA-IB-7651 TCGA-US-A77E 
       66.94        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        39.98        16.80         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
          14.14            0.03 
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
          66.94           75.12 
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
         18.870          14.005 
[1] "14.1 - 66.9 (18.9)" "0.0 - 75.1 (14.0)" 
[1] "hr=" "1.1"
D163V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZBTB4 MUTATED          0        0         0         3         0        1
  ZBTB4 WILD-TYPE        3        8        23       100         4        3
D163V3, multiclass
           clus
vv          ZBTB4 MUTATED ZBTB4 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              1               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
  ZBTB4 MUTATED     0   0     4
  ZBTB4 WILD-TYPE   4  16   121
D163V4, multiclass
       clus
vv      ZBTB4 MUTATED ZBTB4 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D163V5, binary
                 cls
clus                0   1
  ZBTB4 MUTATED     1   3
  ZBTB4 WILD-TYPE  36 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB4 MUTATED      1    3
  ZBTB4 WILD-TYPE   36  105
   clus
vv  ZBTB4 MUTATED ZBTB4 WILD-TYPE
  0             1              36
  1             3             105
[1] 2 2
[1] FALSE
D163V6, binary
                 cls
clus               0  1
  ZBTB4 MUTATED    2  1
  ZBTB4 WILD-TYPE 64  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB4 MUTATED      2    1
  ZBTB4 WILD-TYPE   64    3
   clus
vv  ZBTB4 MUTATED ZBTB4 WILD-TYPE
  0             2              64
  1             1               3
[1] 2 2
[1] FALSE
D163V7, binary
                 cls
clus               0  1
  ZBTB4 MUTATED    3  1
  ZBTB4 WILD-TYPE 64 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB4 MUTATED      3    1
  ZBTB4 WILD-TYPE   64   78
        clus
vv       ZBTB4 MUTATED ZBTB4 WILD-TYPE
  FEMALE             3              64
  MALE               1              78
[1] 2 2
[1] FALSE
D163V8, binary
                 cls
clus               0  1
  ZBTB4 MUTATED    3  0
  ZBTB4 WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB4 MUTATED      3    0
  ZBTB4 WILD-TYPE   91   36
     clus
vv    ZBTB4 MUTATED ZBTB4 WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZBTB4 MUTATED                                     3
  ZBTB4 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZBTB4 MUTATED                                       1
  ZBTB4 WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZBTB4 MUTATED                                                  0
  ZBTB4 WILD-TYPE                                                2
D163V9, multiclass
                                                  clus
vv                                                 ZBTB4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ZBTB4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D163V10, continuous
[1] "Remove cluster labels:" "ZBTB4 MUTATED"         
clus
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              1              49 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
     TCGA-YY-A8LH 
"ZBTB4 WILD-TYPE" 
D163V11, continuous
[1] "Remove cluster labels:" "ZBTB4 MUTATED"         
clus
  ZBTB4 MUTATED ZBTB4 WILD-TYPE 
              1              39 
     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-XN-A8T5      TCGA-YY-A8LH 
"ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" "ZBTB4 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ZBTB4 MUTATED    2  2  0  0
  ZBTB4 WILD-TYPE 77 48  4  3
D163V12, multiclass
    clus
vv   ZBTB4 MUTATED ZBTB4 WILD-TYPE
  R0             2              77
  R1             2              48
  R2             0               4
  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"
D163V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZBTB4 MUTATED       1                         0     3
  ZBTB4 WILD-TYPE     8                         5   125
D163V14, multiclass
                           clus
vv                          ZBTB4 MUTATED ZBTB4 WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V15, binary
                 cls
clus                0   1
  ZBTB4 MUTATED     0   3
  ZBTB4 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB4 MUTATED      0    3
  ZBTB4 WILD-TYPE    5  102
                        clus
vv                       ZBTB4 MUTATED ZBTB4 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(164) Variable = MLL5 MUTATION ANALYSIS
D164V1, survival
                sevent
clus2             0  1
  MLL5 MUTATED    1  3
  MLL5 WILD-TYPE 67 73
  MLL5 MUTATED MLL5 WILD-TYPE 
             4            140 
  MLL5 MUTATED MLL5 WILD-TYPE 
             3             73 
$`MLL5 MUTATED`
TCGA-HZ-7919 TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7885 
       19.50        20.19        19.82        41.33 

$`MLL5 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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7922 TCGA-HZ-7926 
       66.94         8.28        30.25        17.49         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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  MLL5 MUTATED MLL5 WILD-TYPE 
         19.50           0.03 
  MLL5 MUTATED MLL5 WILD-TYPE 
         41.33          75.12 
  MLL5 MUTATED MLL5 WILD-TYPE 
        20.005         13.990 
[1] "19.5 - 41.3 (20.0)" "0.0 - 75.1 (14.0)" 
[1] "hr=" "1.1"
D164V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MLL5 MUTATED          0        0         0         4         0        0
  MLL5 WILD-TYPE        3        8        23        99         4        4
D164V3, multiclass
           clus
vv          MLL5 MUTATED MLL5 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            4             99
  STAGE III            0              4
  STAGE IV             0              4
[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
  MLL5 MUTATED     0   0     4
  MLL5 WILD-TYPE   4  16   121
D164V4, multiclass
       clus
vv      MLL5 MUTATED MLL5 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D164V5, binary
                cls
clus               0   1
  MLL5 MUTATED     0   4
  MLL5 WILD-TYPE  37 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL5 MUTATED      0    4
  MLL5 WILD-TYPE   37  104
   clus
vv  MLL5 MUTATED MLL5 WILD-TYPE
  0            0             37
  1            4            104
[1] 2 2
[1] FALSE
D164V6, binary
                cls
clus              0  1
  MLL5 MUTATED    3  0
  MLL5 WILD-TYPE 63  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL5 MUTATED      3    0
  MLL5 WILD-TYPE   63    4
   clus
vv  MLL5 MUTATED MLL5 WILD-TYPE
  0            3             63
  1            0              4
[1] 2 2
[1] FALSE
D164V7, binary
                cls
clus              0  1
  MLL5 MUTATED    3  1
  MLL5 WILD-TYPE 64 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL5 MUTATED      3    1
  MLL5 WILD-TYPE   64   78
        clus
vv       MLL5 MUTATED MLL5 WILD-TYPE
  FEMALE            3             64
  MALE              1             78
[1] 2 2
[1] FALSE
D164V8, binary
                cls
clus              0  1
  MLL5 MUTATED    3  0
  MLL5 WILD-TYPE 91 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL5 MUTATED      3    0
  MLL5 WILD-TYPE   91   36
     clus
vv    MLL5 MUTATED MLL5 WILD-TYPE
  NO             3             91
  YES            0             36
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MLL5 MUTATED                                     4
  MLL5 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MLL5 MUTATED                                       0
  MLL5 WILD-TYPE                                    13
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MLL5 MUTATED                                                  0
  MLL5 WILD-TYPE                                                2
D164V9, multiclass
                                                  clus
vv                                                 MLL5 MUTATED MLL5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0             13
  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"
D164V10, continuous
[1] "Remove cluster labels:" "MLL5 MUTATED"          
clus
  MLL5 MUTATED MLL5 WILD-TYPE 
             2             48 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-HV-AA8V     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7886     TCGA-IB-7887 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
D164V11, continuous
[1] "Remove cluster labels:" "MLL5 MUTATED"          
clus
  MLL5 MUTATED MLL5 WILD-TYPE 
             2             38 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A77Q     TCGA-HZ-A8P0     TCGA-HZ-A8P1 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-IB-7644     TCGA-IB-7649     TCGA-IB-7886     TCGA-IB-7891 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS     TCGA-IB-A6UF 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ     TCGA-IB-AAUS 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5     TCGA-OE-A75W 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI     TCGA-XD-AAUL 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
    TCGA-XN-A8T5     TCGA-YY-A8LH 
"MLL5 WILD-TYPE" "MLL5 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  MLL5 MUTATED    3  1  0  0
  MLL5 WILD-TYPE 76 49  4  3
D164V12, multiclass
    clus
vv   MLL5 MUTATED MLL5 WILD-TYPE
  R0            3             76
  R1            1             49
  R2            0              4
  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"
D164V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL5 MUTATED       0                         0     4
  MLL5 WILD-TYPE     9                         5   124
D164V14, multiclass
                           clus
vv                          MLL5 MUTATED MLL5 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V15, binary
                cls
clus               0   1
  MLL5 MUTATED     0   4
  MLL5 WILD-TYPE   5 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL5 MUTATED      0    4
  MLL5 WILD-TYPE    5  101
                        clus
vv                       MLL5 MUTATED MLL5 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(165) Variable = ADORA3 MUTATION ANALYSIS
D165V1, survival
                  sevent
clus2               0  1
  ADORA3 MUTATED    3  2
  ADORA3 WILD-TYPE 65 74
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               5              139 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               2               74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-7893 TCGA-IB-7897 TCGA-IB-8126 TCGA-IB-A5SO 
       15.81        19.66         3.85        15.98         2.47        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-LB-A8F3 TCGA-LB-A9Q5 
        6.02        11.11         7.40         9.44        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ADORA3 MUTATED ADORA3 WILD-TYPE 
            8.05             0.03 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
           21.30            75.12 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
           17.16            14.17 
[1] "8.1 - 21.3 (17.2)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.3"
D165V2, 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        3        8        23        98         4        4
D165V3, multiclass
           clus
vv          ADORA3 MUTATED ADORA3 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              5               98
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   120
D165V4, multiclass
       clus
vv      ADORA3 MUTATED ADORA3 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D165V5, binary
                  cls
clus                 0   1
  ADORA3 MUTATED     0   5
  ADORA3 WILD-TYPE  37 103
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      0    5
  ADORA3 WILD-TYPE   37  103
   clus
vv  ADORA3 MUTATED ADORA3 WILD-TYPE
  0              0               37
  1              5              103
[1] 2 2
[1] FALSE
D165V6, binary
                  cls
clus                0  1
  ADORA3 MUTATED    4  0
  ADORA3 WILD-TYPE 62  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      4    0
  ADORA3 WILD-TYPE   62    4
   clus
vv  ADORA3 MUTATED ADORA3 WILD-TYPE
  0              4               62
  1              0                4
[1] 2 2
[1] FALSE
D165V7, binary
                  cls
clus                0  1
  ADORA3 MUTATED    3  2
  ADORA3 WILD-TYPE 64 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      3    2
  ADORA3 WILD-TYPE   64   77
        clus
vv       ADORA3 MUTATED ADORA3 WILD-TYPE
  FEMALE              3               64
  MALE                2               77
[1] 2 2
[1] FALSE
D165V8, binary
                  cls
clus                0  1
  ADORA3 MUTATED    5  0
  ADORA3 WILD-TYPE 89 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      5    0
  ADORA3 WILD-TYPE   89   36
     clus
vv    ADORA3 MUTATED ADORA3 WILD-TYPE
  NO               5               89
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ADORA3 MUTATED                                     5
  ADORA3 WILD-TYPE                                 125
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ADORA3 MUTATED                                       0
  ADORA3 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ADORA3 MUTATED                                                  0
  ADORA3 WILD-TYPE                                                2
D165V9, 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                           125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D165V10, continuous
D165V11, continuous
                  vv
clus               R0 R1 R2 RX
  ADORA3 MUTATED    3  2  0  0
  ADORA3 WILD-TYPE 76 48  4  3
D165V12, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  R0              3               76
  R1              2               48
  R2              0                4
  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"
D165V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADORA3 MUTATED       0                         1     4
  ADORA3 WILD-TYPE     9                         4   124
D165V14, multiclass
                           clus
vv                          ADORA3 MUTATED ADORA3 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V15, binary
                  cls
clus                 0   1
  ADORA3 MUTATED     0   5
  ADORA3 WILD-TYPE   5 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      0    5
  ADORA3 WILD-TYPE    5  100
                        clus
vv                       ADORA3 MUTATED ADORA3 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5              100
[1] 2 2
[1] FALSE

Clustering(166) Variable = ARHGAP9 MUTATION ANALYSIS
D166V1, survival
                   sevent
clus2                0  1
  ARHGAP9 MUTATED    2  2
  ARHGAP9 WILD-TYPE 66 74
  ARHGAP9 MUTATED ARHGAP9 WILD-TYPE 
                4               140 
  ARHGAP9 MUTATED ARHGAP9 WILD-TYPE 
                2                74 
$`ARHGAP9 MUTATED`
TCGA-IB-7651 TCGA-IB-A6UF TCGA-US-A77G TCGA-XN-A8T5 
       19.82        21.90         0.39        23.67 

$`ARHGAP9 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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
        0.23        19.82        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-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        24.23        17.26 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG 
       23.08        22.85        39.98        16.80        14.14        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        12.03        16.37        31.27        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ARHGAP9 MUTATED ARHGAP9 WILD-TYPE 
             0.39              0.03 
  ARHGAP9 MUTATED ARHGAP9 WILD-TYPE 
            23.67             75.12 
  ARHGAP9 MUTATED ARHGAP9 WILD-TYPE 
           20.860            14.155 
[1] "0.4 - 23.7 (20.9)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.3"
D166V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ARHGAP9 MUTATED          0        1         0         3         0        0
  ARHGAP9 WILD-TYPE        3        7        23       100         4        4
D166V3, multiclass
           clus
vv          ARHGAP9 MUTATED ARHGAP9 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                1                 7
  STAGE IIA               0                23
  STAGE IIB               3               100
  STAGE III               0                 4
  STAGE IV                0                 4
[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
  ARHGAP9 MUTATED     0   1     3
  ARHGAP9 WILD-TYPE   4  15   122
D166V4, multiclass
       clus
vv      ARHGAP9 MUTATED ARHGAP9 WILD-TYPE
  T1                  0                 4
  T2                  1                15
  T3+T4               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"
D166V5, binary
                   cls
clus                  0   1
  ARHGAP9 MUTATED     1   3
  ARHGAP9 WILD-TYPE  36 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP9 MUTATED      1    3
  ARHGAP9 WILD-TYPE   36  105
   clus
vv  ARHGAP9 MUTATED ARHGAP9 WILD-TYPE
  0               1                36
  1               3               105
[1] 2 2
[1] FALSE
D166V6, binary
                   cls
clus                 0  1
  ARHGAP9 MUTATED    3  0
  ARHGAP9 WILD-TYPE 63  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP9 MUTATED      3    0
  ARHGAP9 WILD-TYPE   63    4
   clus
vv  ARHGAP9 MUTATED ARHGAP9 WILD-TYPE
  0               3                63
  1               0                 4
[1] 2 2
[1] FALSE
D166V7, binary
                   cls
clus                 0  1
  ARHGAP9 MUTATED    2  2
  ARHGAP9 WILD-TYPE 65 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP9 MUTATED      2    2
  ARHGAP9 WILD-TYPE   65   77
        clus
vv       ARHGAP9 MUTATED ARHGAP9 WILD-TYPE
  FEMALE               2                65
  MALE                 2                77
[1] 2 2
[1] FALSE
D166V8, binary
                   cls
clus                 0  1
  ARHGAP9 MUTATED    3  1
  ARHGAP9 WILD-TYPE 91 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP9 MUTATED      3    1
  ARHGAP9 WILD-TYPE   91   35
     clus
vv    ARHGAP9 MUTATED ARHGAP9 WILD-TYPE
  NO                3                91
  YES               1                35
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARHGAP9 MUTATED                                     3
  ARHGAP9 WILD-TYPE                                 127
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARHGAP9 MUTATED                                       1
  ARHGAP9 WILD-TYPE                                    12
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARHGAP9 MUTATED                                                  0
  ARHGAP9 WILD-TYPE                                                2
D166V9, multiclass
                                                  clus
vv                                                 ARHGAP9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 ARHGAP9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           12
  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"
D166V10, continuous
D166V11, continuous
                   vv
clus                R0 R1 R2 RX
  ARHGAP9 MUTATED    2  2  0  0
  ARHGAP9 WILD-TYPE 77 48  4  3
D166V12, multiclass
    clus
vv   ARHGAP9 MUTATED ARHGAP9 WILD-TYPE
  R0               2                77
  R1               2                48
  R2               0                 4
  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"
D166V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP9 MUTATED       0                         0     4
  ARHGAP9 WILD-TYPE     9                         5   124
D166V14, multiclass
                           clus
vv                          ARHGAP9 MUTATED ARHGAP9 WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   4               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V15, binary
                   cls
clus                  0   1
  ARHGAP9 MUTATED     1   3
  ARHGAP9 WILD-TYPE   4 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP9 MUTATED      1    3
  ARHGAP9 WILD-TYPE    4  102
                        clus
vv                       ARHGAP9 MUTATED ARHGAP9 WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               3               102
[1] 2 2
[1] FALSE

Clustering(167) Variable = ANKRD30A MUTATION ANALYSIS
D167V1, survival
                    sevent
clus2                 0  1
  ANKRD30A MUTATED    4  4
  ANKRD30A WILD-TYPE 64 72
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 8                136 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 4                 72 
$`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        42.31        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        58.98        43.50        20.84         7.36        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7644 
       21.60         5.26         1.08         0.23        19.82        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-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-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        24.23 
TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A77E TCGA-US-A77G 
       17.26        23.08        22.85        39.98        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       11.51        12.76        66.28        15.35 

  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
              1.35               0.03 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
             24.26              75.12 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
            13.365             14.285 
[1] "1.4 - 24.3 (13.4)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.1"
D167V2, 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        3        8        23        95         4        4
D167V3, multiclass
           clus
vv          ANKRD30A MUTATED ANKRD30A WILD-TYPE
  STAGE IA                 0                  3
  STAGE IB                 0                  8
  STAGE IIA                0                 23
  STAGE IIB                8                 95
  STAGE III                0                  4
  STAGE IV                 0                  4
[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   3  16   118
D167V4, multiclass
       clus
vv      ANKRD30A MUTATED ANKRD30A WILD-TYPE
  T1                   1                  3
  T2                   0                 16
  T3+T4                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"
D167V5, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED     0   8
  ANKRD30A WILD-TYPE  37 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      0    8
  ANKRD30A WILD-TYPE   37  100
   clus
vv  ANKRD30A MUTATED ANKRD30A WILD-TYPE
  0                0                 37
  1                8                100
[1] 2 2
[1] FALSE
D167V6, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    2  0
  ANKRD30A WILD-TYPE 64  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      2    0
  ANKRD30A WILD-TYPE   64    4
   clus
vv  ANKRD30A MUTATED ANKRD30A WILD-TYPE
  0                2                 64
  1                0                  4
[1] 2 2
[1] FALSE
D167V7, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    3  5
  ANKRD30A WILD-TYPE 64 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      3    5
  ANKRD30A WILD-TYPE   64   74
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  FEMALE                3                 64
  MALE                  5                 74
[1] 2 2
[1] FALSE
D167V8, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    4  2
  ANKRD30A WILD-TYPE 90 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      4    2
  ANKRD30A WILD-TYPE   90   34
     clus
vv    ANKRD30A MUTATED ANKRD30A WILD-TYPE
  NO                 4                 90
  YES                2                 34
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANKRD30A MUTATED                                     7
  ANKRD30A WILD-TYPE                                 123
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANKRD30A MUTATED                                       1
  ANKRD30A WILD-TYPE                                    12
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANKRD30A MUTATED                                                  0
  ANKRD30A WILD-TYPE                                                2
D167V9, 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                             123
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            12
  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"
D167V10, continuous
D167V11, continuous
                    vv
clus                 R0 R1 R2 RX
  ANKRD30A MUTATED    6  2  0  0
  ANKRD30A WILD-TYPE 73 48  4  3
D167V12, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  R0                6                 73
  R1                2                 48
  R2                0                  4
  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"
D167V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD30A MUTATED       0                         0     8
  ANKRD30A WILD-TYPE     9                         5   120
D167V14, multiclass
                           clus
vv                          ANKRD30A MUTATED ANKRD30A WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    8                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"
D167V15, binary
                    cls
clus                  0  1
  ANKRD30A MUTATED    0  7
  ANKRD30A WILD-TYPE  5 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED      0    7
  ANKRD30A WILD-TYPE    5   98
                        clus
vv                       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                7                 98
[1] 2 2
[1] FALSE

Clustering(168) Variable = KIF4B MUTATION ANALYSIS
D168V1, survival
                 sevent
clus2              0  1
  KIF4B MUTATED    2  3
  KIF4B WILD-TYPE 66 73
  KIF4B MUTATED KIF4B WILD-TYPE 
              5             139 
  KIF4B MUTATED KIF4B WILD-TYPE 
              3              73 
$`KIF4B MUTATED`
TCGA-HV-A5A6 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A6UG TCGA-RB-AA9M 
       66.94        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
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-A7LX 
       15.85         7.20        15.12        20.88        21.90         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-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
       15.32        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  KIF4B MUTATED KIF4B WILD-TYPE 
           1.35            0.03 
  KIF4B MUTATED KIF4B WILD-TYPE 
          66.94           75.12 
  KIF4B MUTATED KIF4B WILD-TYPE 
          19.82           14.17 
[1] "1.4 - 66.9 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.3"
D168V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KIF4B MUTATED          0        0         0         5         0        0
  KIF4B WILD-TYPE        3        8        23        98         4        4
D168V3, multiclass
           clus
vv          KIF4B MUTATED KIF4B WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             5              98
  STAGE III             0               4
  STAGE IV              0               4
[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     4
  KIF4B WILD-TYPE   3  16   121
D168V4, multiclass
       clus
vv      KIF4B MUTATED KIF4B WILD-TYPE
  T1                1               3
  T2                0              16
  T3+T4             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"
D168V5, binary
                 cls
clus                0   1
  KIF4B MUTATED     0   5
  KIF4B WILD-TYPE  37 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF4B MUTATED      0    5
  KIF4B WILD-TYPE   37  103
   clus
vv  KIF4B MUTATED KIF4B WILD-TYPE
  0             0              37
  1             5             103
[1] 2 2
[1] FALSE
D168V6, binary
                 cls
clus               0  1
  KIF4B MUTATED    4  0
  KIF4B WILD-TYPE 62  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF4B MUTATED      4    0
  KIF4B WILD-TYPE   62    4
   clus
vv  KIF4B MUTATED KIF4B WILD-TYPE
  0             4              62
  1             0               4
[1] 2 2
[1] FALSE
D168V7, binary
                 cls
clus               0  1
  KIF4B MUTATED    3  2
  KIF4B WILD-TYPE 64 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF4B MUTATED      3    2
  KIF4B WILD-TYPE   64   77
        clus
vv       KIF4B MUTATED KIF4B WILD-TYPE
  FEMALE             3              64
  MALE               2              77
[1] 2 2
[1] FALSE
D168V8, binary
                 cls
clus               0  1
  KIF4B MUTATED    4  1
  KIF4B WILD-TYPE 90 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF4B MUTATED      4    1
  KIF4B WILD-TYPE   90   35
     clus
vv    KIF4B MUTATED KIF4B WILD-TYPE
  NO              4              90
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIF4B MUTATED                                     5
  KIF4B WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIF4B MUTATED                                       0
  KIF4B WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIF4B MUTATED                                                  0
  KIF4B WILD-TYPE                                                2
D168V9, multiclass
                                                  clus
vv                                                 KIF4B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 KIF4B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D168V10, continuous
D168V11, continuous
                 vv
clus              R0 R1 R2 RX
  KIF4B MUTATED    4  1  0  0
  KIF4B WILD-TYPE 75 49  4  3
D168V12, multiclass
    clus
vv   KIF4B MUTATED KIF4B WILD-TYPE
  R0             4              75
  R1             1              49
  R2             0               4
  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"
D168V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIF4B MUTATED       1                         0     4
  KIF4B WILD-TYPE     8                         5   124
D168V14, multiclass
                           clus
vv                          KIF4B MUTATED KIF4B WILD-TYPE
  ASIAN                                 1               8
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 4             124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V15, binary
                 cls
clus                0   1
  KIF4B MUTATED     0   4
  KIF4B WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF4B MUTATED      0    4
  KIF4B WILD-TYPE    5  101
                        clus
vv                       KIF4B MUTATED KIF4B WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(169) Variable = ATP2C2 MUTATION ANALYSIS
D169V1, survival
                  sevent
clus2               0  1
  ATP2C2 MUTATED    2  2
  ATP2C2 WILD-TYPE 66 74
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               4              140 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               2               74 
$`ATP2C2 MUTATED`
TCGA-3A-A9IH TCGA-FB-AAPS TCGA-IB-7651 TCGA-US-A77G 
       33.57         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        42.31        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        58.98        43.50        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        24.43        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        12.66        16.37         0.03        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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-XD-AAUG TCGA-XD-AAUH 
       22.85        39.98        16.80        14.14        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
            0.39             0.03 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
           33.57            75.12 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
          13.660           14.285 
[1] "0.4 - 33.6 (13.7)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1"  
D169V2, 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        2        8        23       100         4        4
D169V3, multiclass
           clus
vv          ATP2C2 MUTATED ATP2C2 WILD-TYPE
  STAGE IA               1                2
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   3  15   123
D169V4, multiclass
       clus
vv      ATP2C2 MUTATED ATP2C2 WILD-TYPE
  T1                 1                3
  T2                 1               15
  T3+T4              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"
D169V5, binary
                  cls
clus                 0   1
  ATP2C2 MUTATED     1   3
  ATP2C2 WILD-TYPE  36 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      1    3
  ATP2C2 WILD-TYPE   36  105
   clus
vv  ATP2C2 MUTATED ATP2C2 WILD-TYPE
  0              1               36
  1              3              105
[1] 2 2
[1] FALSE
D169V6, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    1  0
  ATP2C2 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      1    0
  ATP2C2 WILD-TYPE   65    4
   clus
vv  ATP2C2 MUTATED ATP2C2 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D169V7, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    3  1
  ATP2C2 WILD-TYPE 64 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      3    1
  ATP2C2 WILD-TYPE   64   78
        clus
vv       ATP2C2 MUTATED ATP2C2 WILD-TYPE
  FEMALE              3               64
  MALE                1               78
[1] 2 2
[1] FALSE
D169V8, binary
                  cls
clus                0  1
  ATP2C2 MUTATED    3  1
  ATP2C2 WILD-TYPE 91 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      3    1
  ATP2C2 WILD-TYPE   91   35
     clus
vv    ATP2C2 MUTATED ATP2C2 WILD-TYPE
  NO               3               91
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATP2C2 MUTATED                                     4
  ATP2C2 WILD-TYPE                                 126
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATP2C2 MUTATED                                       0
  ATP2C2 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATP2C2 MUTATED                                                  0
  ATP2C2 WILD-TYPE                                                2
D169V9, 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                           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D169V10, continuous
[1] "Remove cluster labels:" "ATP2C2 MUTATED"        
clus
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               2               48 
      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-HV-AA8V 
"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-7887 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
D169V11, continuous
[1] "Remove cluster labels:" "ATP2C2 MUTATED"        
clus
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"ATP2C2 WILD-TYPE" "ATP2C2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ATP2C2 MUTATED    4  0  0  0
  ATP2C2 WILD-TYPE 75 50  4  3
D169V12, multiclass
    clus
vv   ATP2C2 MUTATED ATP2C2 WILD-TYPE
  R0              4               75
  R1              0               50
  R2              0                4
  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"
D169V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATP2C2 MUTATED       0                         0     4
  ATP2C2 WILD-TYPE     9                         5   124
D169V14, multiclass
                           clus
vv                          ATP2C2 MUTATED ATP2C2 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V15, binary
                  cls
clus                 0   1
  ATP2C2 MUTATED     0   4
  ATP2C2 WILD-TYPE   5 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      0    4
  ATP2C2 WILD-TYPE    5  101
                        clus
vv                       ATP2C2 MUTATED ATP2C2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              101
[1] 2 2
[1] FALSE

Clustering(170) Variable = POM121 MUTATION ANALYSIS
D170V1, survival
                  sevent
clus2               0  1
  POM121 MUTATED    2  3
  POM121 WILD-TYPE 66 73
  POM121 MUTATED POM121 WILD-TYPE 
               5              139 
  POM121 MUTATED POM121 WILD-TYPE 
               3               73 
$`POM121 MUTATED`
TCGA-HZ-7922 TCGA-HZ-A9TJ TCGA-IB-7651 TCGA-IB-A5SQ TCGA-LB-A9Q5 
        0.13        19.82        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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7925 
       66.94         8.28        30.25        17.49        19.50        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        19.59         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-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-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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  POM121 MUTATED POM121 WILD-TYPE 
            0.13             0.03 
  POM121 MUTATED POM121 WILD-TYPE 
           19.82            75.12 
  POM121 MUTATED POM121 WILD-TYPE 
           10.29            14.40 
[1] "0.1 - 19.8 (10.3)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.6"
D170V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  POM121 MUTATED          0        1         0         3         0        1
  POM121 WILD-TYPE        3        7        23       100         4        3
D170V3, multiclass
           clus
vv          POM121 MUTATED POM121 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               1                7
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               1                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     4
  POM121 WILD-TYPE   4  15   121
D170V4, multiclass
       clus
vv      POM121 MUTATED POM121 WILD-TYPE
  T1                 0                4
  T2                 1               15
  T3+T4              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"
D170V5, binary
                  cls
clus                 0   1
  POM121 MUTATED     2   3
  POM121 WILD-TYPE  35 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      2    3
  POM121 WILD-TYPE   35  105
   clus
vv  POM121 MUTATED POM121 WILD-TYPE
  0              2               35
  1              3              105
[1] 2 2
[1] FALSE
D170V6, binary
                  cls
clus                0  1
  POM121 MUTATED    2  1
  POM121 WILD-TYPE 64  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      2    1
  POM121 WILD-TYPE   64    3
   clus
vv  POM121 MUTATED POM121 WILD-TYPE
  0              2               64
  1              1                3
[1] 2 2
[1] FALSE
D170V7, binary
                  cls
clus                0  1
  POM121 MUTATED    4  1
  POM121 WILD-TYPE 63 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      4    1
  POM121 WILD-TYPE   63   78
        clus
vv       POM121 MUTATED POM121 WILD-TYPE
  FEMALE              4               63
  MALE                1               78
[1] 2 2
[1] FALSE
D170V8, binary
                  cls
clus                0  1
  POM121 MUTATED    3  1
  POM121 WILD-TYPE 91 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      3    1
  POM121 WILD-TYPE   91   35
     clus
vv    POM121 MUTATED POM121 WILD-TYPE
  NO               3               91
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  POM121 MUTATED                                     4
  POM121 WILD-TYPE                                 126
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  POM121 MUTATED                                       1
  POM121 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  POM121 MUTATED                                                  0
  POM121 WILD-TYPE                                                2
D170V9, multiclass
                                                  clus
vv                                                 POM121 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 POM121 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D170V10, continuous
[1] "Remove cluster labels:" "POM121 MUTATED"        
clus
  POM121 MUTATED POM121 WILD-TYPE 
               2               48 
      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-HV-AA8V       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-7887       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-A5SS       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
D170V11, continuous
[1] "Remove cluster labels:" "POM121 MUTATED"        
clus
  POM121 MUTATED POM121 WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  POM121 MUTATED    5  0  0  0
  POM121 WILD-TYPE 74 50  4  3
D170V12, multiclass
    clus
vv   POM121 MUTATED POM121 WILD-TYPE
  R0              5               74
  R1              0               50
  R2              0                4
  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"
D170V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POM121 MUTATED       0                         0     5
  POM121 WILD-TYPE     9                         5   123
D170V14, multiclass
                           clus
vv                          POM121 MUTATED POM121 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              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"
D170V15, binary
                  cls
clus                 0   1
  POM121 MUTATED     0   5
  POM121 WILD-TYPE   5 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      0    5
  POM121 WILD-TYPE    5  100
                        clus
vv                       POM121 MUTATED POM121 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5              100
[1] 2 2
[1] FALSE

Clustering(171) Variable = DDB1 MUTATION ANALYSIS
D171V1, survival
                sevent
clus2             0  1
  DDB1 MUTATED    3  2
  DDB1 WILD-TYPE 65 74
  DDB1 MUTATED DDB1 WILD-TYPE 
             5            139 
  DDB1 MUTATED DDB1 WILD-TYPE 
             2             74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A8P1 
       10.13         6.38        21.60         5.26        10.85         0.23 
TCGA-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 TCGA-IB-7652 
       19.82        12.95         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-AA2A 
       12.46        10.29        19.20         8.78        15.45         3.12 
TCGA-RB-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 
       15.32         9.40        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-Z5-AAPL 
       15.35 

  DDB1 MUTATED DDB1 WILD-TYPE 
          1.08           0.03 
  DDB1 MUTATED DDB1 WILD-TYPE 
         66.28          75.12 
  DDB1 MUTATED DDB1 WILD-TYPE 
         19.82          14.17 
[1] "1.1 - 66.3 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "2.2"
D171V2, 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        3        8        23        98         4        4
D171V3, multiclass
           clus
vv          DDB1 MUTATED DDB1 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            5             98
  STAGE III            0              4
  STAGE IV             0              4
[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   4  16   120
D171V4, multiclass
       clus
vv      DDB1 MUTATED DDB1 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D171V5, binary
                cls
clus               0   1
  DDB1 MUTATED     0   5
  DDB1 WILD-TYPE  37 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      0    5
  DDB1 WILD-TYPE   37  103
   clus
vv  DDB1 MUTATED DDB1 WILD-TYPE
  0            0             37
  1            5            103
[1] 2 2
[1] FALSE
D171V6, binary
                cls
clus              0  1
  DDB1 MUTATED    2  0
  DDB1 WILD-TYPE 64  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      2    0
  DDB1 WILD-TYPE   64    4
   clus
vv  DDB1 MUTATED DDB1 WILD-TYPE
  0            2             64
  1            0              4
[1] 2 2
[1] FALSE
D171V7, binary
                cls
clus              0  1
  DDB1 MUTATED    4  1
  DDB1 WILD-TYPE 63 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      4    1
  DDB1 WILD-TYPE   63   78
        clus
vv       DDB1 MUTATED DDB1 WILD-TYPE
  FEMALE            4             63
  MALE              1             78
[1] 2 2
[1] FALSE
D171V8, binary
                cls
clus              0  1
  DDB1 MUTATED    3  1
  DDB1 WILD-TYPE 91 35
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      3    1
  DDB1 WILD-TYPE   91   35
     clus
vv    DDB1 MUTATED DDB1 WILD-TYPE
  NO             3             91
  YES            1             35
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DDB1 MUTATED                                     4
  DDB1 WILD-TYPE                                 126
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DDB1 MUTATED                                       1
  DDB1 WILD-TYPE                                    12
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DDB1 MUTATED                                                  0
  DDB1 WILD-TYPE                                                2
D171V9, multiclass
                                                  clus
vv                                                 DDB1 MUTATED DDB1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4            126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             12
  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"
D171V10, continuous
D171V11, continuous
                vv
clus             R0 R1 R2 RX
  DDB1 MUTATED    5  0  0  0
  DDB1 WILD-TYPE 74 50  4  3
D171V12, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  R0            5             74
  R1            0             50
  R2            0              4
  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"
D171V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DDB1 MUTATED       0                         0     4
  DDB1 WILD-TYPE     9                         5   124
D171V14, multiclass
                           clus
vv                          DDB1 MUTATED DDB1 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V15, binary
                cls
clus               0   1
  DDB1 MUTATED     0   4
  DDB1 WILD-TYPE   5 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      0    4
  DDB1 WILD-TYPE    5  101
                        clus
vv                       DDB1 MUTATED DDB1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(172) Variable = NUP54 MUTATION ANALYSIS
D172V1, survival
                 sevent
clus2              0  1
  NUP54 MUTATED    0  3
  NUP54 WILD-TYPE 68 73
  NUP54 MUTATED NUP54 WILD-TYPE 
              3             141 
  NUP54 MUTATED NUP54 WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H 
        9.83        12.43        14.93        17.92        21.70        16.14 
TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
       10.13         6.38        21.60         5.26        10.85         1.08 
TCGA-HZ-A8P1 TCGA-HZ-A9TJ TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
        0.23        19.82        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-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-PZ-A5RE TCGA-Q3-A5QY 
       12.92        12.46        10.29        19.20        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  NUP54 MUTATED NUP54 WILD-TYPE 
           8.78            0.03 
  NUP54 MUTATED NUP54 WILD-TYPE 
          19.82           75.12 
  NUP54 MUTATED NUP54 WILD-TYPE 
          12.95           14.40 
[1] "8.8 - 19.8 (12.9)" "0.0 - 75.1 (14.4)"
[1] "hr=" "2.4"
D172V2, 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        3        8        22       102         4        3
D172V3, multiclass
           clus
vv          NUP54 MUTATED NUP54 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             1             102
  STAGE III             0               4
  STAGE IV              1               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
  NUP54 MUTATED     0   0     3
  NUP54 WILD-TYPE   4  16   122
D172V4, multiclass
       clus
vv      NUP54 MUTATED NUP54 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D172V5, binary
                 cls
clus                0   1
  NUP54 MUTATED     1   2
  NUP54 WILD-TYPE  36 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      1    2
  NUP54 WILD-TYPE   36  106
   clus
vv  NUP54 MUTATED NUP54 WILD-TYPE
  0             1              36
  1             2             106
[1] 2 2
[1] FALSE
D172V6, binary
                 cls
clus               0  1
  NUP54 MUTATED    2  1
  NUP54 WILD-TYPE 64  3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      2    1
  NUP54 WILD-TYPE   64    3
   clus
vv  NUP54 MUTATED NUP54 WILD-TYPE
  0             2              64
  1             1               3
[1] 2 2
[1] FALSE
D172V7, binary
                 cls
clus               0  1
  NUP54 MUTATED    2  1
  NUP54 WILD-TYPE 65 78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      2    1
  NUP54 WILD-TYPE   65   78
        clus
vv       NUP54 MUTATED NUP54 WILD-TYPE
  FEMALE             2              65
  MALE               1              78
[1] 2 2
[1] FALSE
D172V8, binary
                 cls
clus               0  1
  NUP54 MUTATED    2  1
  NUP54 WILD-TYPE 92 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      2    1
  NUP54 WILD-TYPE   92   35
     clus
vv    NUP54 MUTATED NUP54 WILD-TYPE
  NO              2              92
  YES             1              35
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NUP54 MUTATED                                     3
  NUP54 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NUP54 MUTATED                                       0
  NUP54 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NUP54 MUTATED                                                  0
  NUP54 WILD-TYPE                                                2
D172V9, 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                          127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D172V10, continuous
D172V11, continuous
                 vv
clus              R0 R1 R2 RX
  NUP54 MUTATED    2  1  0  0
  NUP54 WILD-TYPE 77 49  4  3
D172V12, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  R0             2              77
  R1             1              49
  R2             0               4
  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"
D172V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUP54 MUTATED       0                         0     3
  NUP54 WILD-TYPE     9                         5   125
D172V14, multiclass
                           clus
vv                          NUP54 MUTATED NUP54 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V15, binary
                 cls
clus                0   1
  NUP54 MUTATED     0   3
  NUP54 WILD-TYPE   5 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      0    3
  NUP54 WILD-TYPE    5  102
                        clus
vv                       NUP54 MUTATED NUP54 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(173) Variable = C14ORF21 MUTATION ANALYSIS
D173V1, survival
                    sevent
clus2                 0  1
  C14ORF21 MUTATED    1  3
  C14ORF21 WILD-TYPE 67 73
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 4                140 
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 3                 73 
$`C14ORF21 MUTATED`
TCGA-2J-AABU TCGA-2L-AAQE TCGA-IB-7651 TCGA-IB-A6UF 
        9.11        22.49        19.82        21.90 

$`C14ORF21 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        42.31        15.91        14.47        14.40 
TCGA-2J-AABV TCGA-2L-AAQA TCGA-2L-AAQI TCGA-2L-AAQJ TCGA-2L-AAQL TCGA-3A-A9I5 
       21.44         4.70         3.39        12.95         9.60        58.98 
TCGA-3A-A9I7 TCGA-3A-A9I9 TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       43.50        20.84         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A6UG TCGA-IB-A7LX 
       15.85         7.20        15.12        20.88         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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
              9.11               0.03 
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
             22.49              75.12 
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
            20.860             14.155 
[1] "9.1 - 22.5 (20.9)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.1"
D173V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  C14ORF21 MUTATED          0        0         0         4         0        0
  C14ORF21 WILD-TYPE        3        8        23        99         4        4
D173V3, multiclass
           clus
vv          C14ORF21 MUTATED C14ORF21 WILD-TYPE
  STAGE IA                 0                  3
  STAGE IB                 0                  8
  STAGE IIA                0                 23
  STAGE IIB                4                 99
  STAGE III                0                  4
  STAGE IV                 0                  4
[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
  C14ORF21 MUTATED     0   0     4
  C14ORF21 WILD-TYPE   4  16   121
D173V4, multiclass
       clus
vv      C14ORF21 MUTATED C14ORF21 WILD-TYPE
  T1                   0                  4
  T2                   0                 16
  T3+T4                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"
D173V5, binary
                    cls
clus                   0   1
  C14ORF21 MUTATED     0   4
  C14ORF21 WILD-TYPE  37 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      0    4
  C14ORF21 WILD-TYPE   37  104
   clus
vv  C14ORF21 MUTATED C14ORF21 WILD-TYPE
  0                0                 37
  1                4                104
[1] 2 2
[1] FALSE
D173V6, binary
                    cls
clus                  0  1
  C14ORF21 MUTATED    4  0
  C14ORF21 WILD-TYPE 62  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      4    0
  C14ORF21 WILD-TYPE   62    4
   clus
vv  C14ORF21 MUTATED C14ORF21 WILD-TYPE
  0                4                 62
  1                0                  4
[1] 2 2
[1] FALSE
D173V7, binary
                    cls
clus                  0  1
  C14ORF21 MUTATED    1  3
  C14ORF21 WILD-TYPE 66 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      1    3
  C14ORF21 WILD-TYPE   66   76
        clus
vv       C14ORF21 MUTATED C14ORF21 WILD-TYPE
  FEMALE                1                 66
  MALE                  3                 76
[1] 2 2
[1] FALSE
D173V8, binary
                    cls
clus                  0  1
  C14ORF21 MUTATED    4  0
  C14ORF21 WILD-TYPE 90 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      4    0
  C14ORF21 WILD-TYPE   90   36
     clus
vv    C14ORF21 MUTATED C14ORF21 WILD-TYPE
  NO                 4                 90
  YES                0                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C14ORF21 MUTATED                                     4
  C14ORF21 WILD-TYPE                                 126
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C14ORF21 MUTATED                                       0
  C14ORF21 WILD-TYPE                                    13
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C14ORF21 MUTATED                                                  0
  C14ORF21 WILD-TYPE                                                2
D173V9, multiclass
                                                  clus
vv                                                 C14ORF21 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 C14ORF21 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            13
  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"
D173V10, continuous
D173V11, continuous
[1] "Remove cluster labels:" "C14ORF21 MUTATED"      
clus
  C14ORF21 MUTATED C14ORF21 WILD-TYPE 
                 2                 38 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IX 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A4P6         TCGA-FB-A5VM 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-AAPS         TCGA-FB-AAPY 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-H6-8124         TCGA-HZ-A77Q         TCGA-HZ-A8P0 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-HZ-A8P1         TCGA-IB-7644         TCGA-IB-7649 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7891 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-LB-A7SX 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUI         TCGA-XD-AAUL 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"C14ORF21 WILD-TYPE" "C14ORF21 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  C14ORF21 MUTATED    3  1  0  0
  C14ORF21 WILD-TYPE 76 49  4  3
D173V12, multiclass
    clus
vv   C14ORF21 MUTATED C14ORF21 WILD-TYPE
  R0                3                 76
  R1                1                 49
  R2                0                  4
  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"
D173V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C14ORF21 MUTATED       0                         0     4
  C14ORF21 WILD-TYPE     9                         5   124
D173V14, multiclass
                           clus
vv                          C14ORF21 MUTATED C14ORF21 WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    4                124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V15, binary
                    cls
clus                   0   1
  C14ORF21 MUTATED     0   2
  C14ORF21 WILD-TYPE   5 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF21 MUTATED      0    2
  C14ORF21 WILD-TYPE    5  103
                        clus
vv                       C14ORF21 MUTATED C14ORF21 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                2                103
[1] 2 2
[1] FALSE

Clustering(174) Variable = LILRB2 MUTATION ANALYSIS
D174V1, survival
                  sevent
clus2               0  1
  LILRB2 MUTATED    0  4
  LILRB2 WILD-TYPE 68 72
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               4              140 
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               4               72 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         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        19.59         3.95 
TCGA-HZ-8315 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I 
        9.83        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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04         3.62        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-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-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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  LILRB2 MUTATED LILRB2 WILD-TYPE 
            7.20             0.03 
  LILRB2 MUTATED LILRB2 WILD-TYPE 
           43.79            75.12 
  LILRB2 MUTATED LILRB2 WILD-TYPE 
          16.125           14.285 
[1] "7.2 - 43.8 (16.1)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.6"
D174V2, 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        3        7        22       101         4        4
D174V3, multiclass
           clus
vv          LILRB2 MUTATED LILRB2 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               1                7
  STAGE IIA              1               22
  STAGE IIB              2              101
  STAGE III              0                4
  STAGE IV               0                4
[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   4  15   122
D174V4, multiclass
       clus
vv      LILRB2 MUTATED LILRB2 WILD-TYPE
  T1                 0                4
  T2                 1               15
  T3+T4              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"
D174V5, binary
                  cls
clus                 0   1
  LILRB2 MUTATED     2   2
  LILRB2 WILD-TYPE  35 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB2 MUTATED      2    2
  LILRB2 WILD-TYPE   35  106
   clus
vv  LILRB2 MUTATED LILRB2 WILD-TYPE
  0              2               35
  1              2              106
[1] 2 2
[1] FALSE
D174V6, binary
                  cls
clus                0  1
  LILRB2 MUTATED    3  0
  LILRB2 WILD-TYPE 63  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB2 MUTATED      3    0
  LILRB2 WILD-TYPE   63    4
   clus
vv  LILRB2 MUTATED LILRB2 WILD-TYPE
  0              3               63
  1              0                4
[1] 2 2
[1] FALSE
D174V7, binary
                  cls
clus                0  1
  LILRB2 MUTATED    4  0
  LILRB2 WILD-TYPE 63 79
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB2 MUTATED      4    0
  LILRB2 WILD-TYPE   63   79
        clus
vv       LILRB2 MUTATED LILRB2 WILD-TYPE
  FEMALE              4               63
  MALE                0               79
[1] 2 2
[1] FALSE
D174V8, binary
                  cls
clus                0  1
  LILRB2 MUTATED    3  1
  LILRB2 WILD-TYPE 91 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB2 MUTATED      3    1
  LILRB2 WILD-TYPE   91   35
     clus
vv    LILRB2 MUTATED LILRB2 WILD-TYPE
  NO               3               91
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  LILRB2 MUTATED                                     4
  LILRB2 WILD-TYPE                                 126
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  LILRB2 MUTATED                                       0
  LILRB2 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  LILRB2 MUTATED                                                  0
  LILRB2 WILD-TYPE                                                2
D174V9, 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                           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D174V10, continuous
[1] "Remove cluster labels:" "LILRB2 MUTATED"        
clus
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               1               49 
      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-HV-AA8V       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-7887       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-A5SS       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-S4-A8RP       TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
      TCGA-YY-A8LH 
"LILRB2 WILD-TYPE" 
D174V11, continuous
[1] "Remove cluster labels:" "LILRB2 MUTATED"        
clus
  LILRB2 MUTATED LILRB2 WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" "LILRB2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  LILRB2 MUTATED    3  1  0  0
  LILRB2 WILD-TYPE 76 49  4  3
D174V12, multiclass
    clus
vv   LILRB2 MUTATED LILRB2 WILD-TYPE
  R0              3               76
  R1              1               49
  R2              0                4
  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"
D174V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LILRB2 MUTATED       0                         1     3
  LILRB2 WILD-TYPE     9                         4   125
D174V14, multiclass
                           clus
vv                          LILRB2 MUTATED LILRB2 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              1                4
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V15, binary
                  cls
clus                 0   1
  LILRB2 MUTATED     0   4
  LILRB2 WILD-TYPE   5 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LILRB2 MUTATED      0    4
  LILRB2 WILD-TYPE    5  101
                        clus
vv                       LILRB2 MUTATED LILRB2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              101
[1] 2 2
[1] FALSE

Clustering(175) Variable = ADAMTSL4 MUTATION ANALYSIS
D175V1, survival
                    sevent
clus2                 0  1
  ADAMTSL4 MUTATED    1  4
  ADAMTSL4 WILD-TYPE 67 72
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                 5                139 
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                 4                 72 
$`ADAMTSL4 MUTATED`
TCGA-FB-A78T TCGA-FB-AAQ0 TCGA-IB-7651 TCGA-IB-7889 TCGA-IB-AAUO 
        0.03        15.55        19.82        15.81         7.86 

$`ADAMTSL4 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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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-AAPS TCGA-FB-AAPU 
        5.88        11.93        12.66        16.37         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-8124 
       34.82        23.54         4.04         5.03         1.02        12.89 
TCGA-H6-A45N TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-7890 TCGA-IB-7891 
       41.33         4.04         3.62        43.79        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
              0.03               0.13 
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
             19.82              75.12 
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
             15.55              14.17 
[1] "0.0 - 19.8 (15.6)" "0.1 - 75.1 (14.2)"
[1] "hr=" "2.2"
D175V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ADAMTSL4 MUTATED          0        0         1         4         0        0
  ADAMTSL4 WILD-TYPE        3        8        22        99         4        4
D175V3, multiclass
           clus
vv          ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  STAGE IA                 0                  3
  STAGE IB                 0                  8
  STAGE IIA                1                 22
  STAGE IIB                4                 99
  STAGE III                0                  4
  STAGE IV                 0                  4
[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
  ADAMTSL4 MUTATED     0   0     5
  ADAMTSL4 WILD-TYPE   4  16   120
D175V4, multiclass
       clus
vv      ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  T1                   0                  4
  T2                   0                 16
  T3+T4                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"
D175V5, binary
                    cls
clus                   0   1
  ADAMTSL4 MUTATED     1   4
  ADAMTSL4 WILD-TYPE  36 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL4 MUTATED      1    4
  ADAMTSL4 WILD-TYPE   36  104
   clus
vv  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  0                1                 36
  1                4                104
[1] 2 2
[1] FALSE
D175V6, binary
                    cls
clus                  0  1
  ADAMTSL4 MUTATED    4  0
  ADAMTSL4 WILD-TYPE 62  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL4 MUTATED      4    0
  ADAMTSL4 WILD-TYPE   62    4
   clus
vv  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  0                4                 62
  1                0                  4
[1] 2 2
[1] FALSE
D175V7, binary
                    cls
clus                  0  1
  ADAMTSL4 MUTATED    4  1
  ADAMTSL4 WILD-TYPE 63 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL4 MUTATED      4    1
  ADAMTSL4 WILD-TYPE   63   78
        clus
vv       ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  FEMALE                4                 63
  MALE                  1                 78
[1] 2 2
[1] FALSE
D175V8, binary
                    cls
clus                  0  1
  ADAMTSL4 MUTATED    4  0
  ADAMTSL4 WILD-TYPE 90 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL4 MUTATED      4    0
  ADAMTSL4 WILD-TYPE   90   36
     clus
vv    ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  NO                 4                 90
  YES                0                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ADAMTSL4 MUTATED                                     5
  ADAMTSL4 WILD-TYPE                                 125
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ADAMTSL4 MUTATED                                       0
  ADAMTSL4 WILD-TYPE                                    13
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ADAMTSL4 MUTATED                                                  0
  ADAMTSL4 WILD-TYPE                                                2
D175V9, multiclass
                                                  clus
vv                                                 ADAMTSL4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 ADAMTSL4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            13
  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"
D175V10, continuous
[1] "Remove cluster labels:" "ADAMTSL4 MUTATED"      
clus
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                 2                 48 
        TCGA-2J-AAB1         TCGA-2J-AABA         TCGA-2J-AABE 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-2J-AABF         TCGA-2J-AABO         TCGA-2J-AABV 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-2L-AAQA         TCGA-2L-AAQE         TCGA-3A-A9I9 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-3A-A9IB         TCGA-3A-A9IX         TCGA-F2-A8YN 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A4P6         TCGA-FB-A5VM 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-FB-AAPY         TCGA-H6-8124 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-H6-A45N         TCGA-HV-AA8V         TCGA-HZ-A77Q 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-HZ-A8P0         TCGA-HZ-A8P1         TCGA-IB-7644 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7885         TCGA-IB-7886 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8126 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-IB-AAUU 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-LB-A7SX         TCGA-LB-A9Q5         TCGA-OE-A75W 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-S4-A8RM         TCGA-S4-A8RP         TCGA-US-A774 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-XD-AAUL         TCGA-XN-A8T5         TCGA-YY-A8LH 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
D175V11, continuous
[1] "Remove cluster labels:" "ADAMTSL4 MUTATED"      
clus
  ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE 
                 2                 38 
        TCGA-2J-AAB1         TCGA-2J-AABE         TCGA-2J-AABF 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-2J-AABO         TCGA-3A-A9IB         TCGA-3A-A9IX 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A4P6         TCGA-FB-A5VM 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-FB-AAPS         TCGA-FB-AAPY         TCGA-H6-8124 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-HZ-A77Q         TCGA-HZ-A8P0         TCGA-HZ-A8P1 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7885 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7891         TCGA-IB-8126 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UF 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-IB-AAUQ 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-IB-AAUS         TCGA-IB-AAUT         TCGA-LB-A7SX 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-LB-A9Q5         TCGA-OE-A75W         TCGA-S4-A8RM 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-US-A774         TCGA-XD-AAUI         TCGA-XD-AAUL 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
        TCGA-XN-A8T5         TCGA-YY-A8LH 
"ADAMTSL4 WILD-TYPE" "ADAMTSL4 WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  ADAMTSL4 MUTATED    4  1  0  0
  ADAMTSL4 WILD-TYPE 75 49  4  3
D175V12, multiclass
    clus
vv   ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  R0                4                 75
  R1                1                 49
  R2                0                  4
  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"
D175V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ADAMTSL4 MUTATED       0                         0     5
  ADAMTSL4 WILD-TYPE     9                         5   123
D175V14, multiclass
                           clus
vv                          ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                0                  5
  WHITE                                    5                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"
D175V15, binary
                    cls
clus                   0   1
  ADAMTSL4 MUTATED     0   5
  ADAMTSL4 WILD-TYPE   5 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL4 MUTATED      0    5
  ADAMTSL4 WILD-TYPE    5  100
                        clus
vv                       ADAMTSL4 MUTATED ADAMTSL4 WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                5                100
[1] 2 2
[1] FALSE

Clustering(176) Variable = ZNF483 MUTATION ANALYSIS
D176V1, survival
                  sevent
clus2               0  1
  ZNF483 MUTATED    2  2
  ZNF483 WILD-TYPE 66 74
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               4              140 
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               2               74 
$`ZNF483 MUTATED`
TCGA-2J-AAB4 TCGA-FB-A78T TCGA-HZ-8315 TCGA-IB-7887 
       23.97         0.03         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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  ZNF483 MUTATED ZNF483 WILD-TYPE 
            0.03             0.13 
  ZNF483 MUTATED ZNF483 WILD-TYPE 
           23.97            75.12 
  ZNF483 MUTATED ZNF483 WILD-TYPE 
           6.725           14.435 
[1] "0.0 - 24.0 (6.7)"  "0.1 - 75.1 (14.4)"
[1] "hr=" "1.5"
D176V2, 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        3        8        22       100         4        4
D176V3, multiclass
           clus
vv          ZNF483 MUTATED ZNF483 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   4  15   122
D176V4, multiclass
       clus
vv      ZNF483 MUTATED ZNF483 WILD-TYPE
  T1                 0                4
  T2                 1               15
  T3+T4              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"
D176V5, binary
                  cls
clus                 0   1
  ZNF483 MUTATED     1   3
  ZNF483 WILD-TYPE  36 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF483 MUTATED      1    3
  ZNF483 WILD-TYPE   36  105
   clus
vv  ZNF483 MUTATED ZNF483 WILD-TYPE
  0              1               36
  1              3              105
[1] 2 2
[1] FALSE
D176V6, binary
                  cls
clus                0  1
  ZNF483 MUTATED    3  0
  ZNF483 WILD-TYPE 63  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF483 MUTATED      3    0
  ZNF483 WILD-TYPE   63    4
   clus
vv  ZNF483 MUTATED ZNF483 WILD-TYPE
  0              3               63
  1              0                4
[1] 2 2
[1] FALSE
D176V7, binary
                  cls
clus                0  1
  ZNF483 MUTATED    3  1
  ZNF483 WILD-TYPE 64 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF483 MUTATED      3    1
  ZNF483 WILD-TYPE   64   78
        clus
vv       ZNF483 MUTATED ZNF483 WILD-TYPE
  FEMALE              3               64
  MALE                1               78
[1] 2 2
[1] FALSE
D176V8, binary
                  cls
clus                0  1
  ZNF483 MUTATED    2  0
  ZNF483 WILD-TYPE 92 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF483 MUTATED      2    0
  ZNF483 WILD-TYPE   92   36
     clus
vv    ZNF483 MUTATED ZNF483 WILD-TYPE
  NO               2               92
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF483 MUTATED                                     3
  ZNF483 WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF483 MUTATED                                       1
  ZNF483 WILD-TYPE                                    12
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF483 MUTATED                                                  0
  ZNF483 WILD-TYPE                                                2
D176V9, 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                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          12
  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"
D176V10, continuous
[1] "Remove cluster labels:" "ZNF483 MUTATED"        
clus
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               2               48 
      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-HV-AA8V 
"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-IB-AAUU       TCGA-LB-A7SX 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
D176V11, continuous
[1] "Remove cluster labels:" "ZNF483 MUTATED"        
clus
  ZNF483 MUTATED ZNF483 WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" "ZNF483 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  ZNF483 MUTATED    2  2  0  0
  ZNF483 WILD-TYPE 77 48  4  3
D176V12, multiclass
    clus
vv   ZNF483 MUTATED ZNF483 WILD-TYPE
  R0              2               77
  R1              2               48
  R2              0                4
  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"
D176V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF483 MUTATED       0                         0     4
  ZNF483 WILD-TYPE     9                         5   124
D176V14, multiclass
                           clus
vv                          ZNF483 MUTATED ZNF483 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  4              124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V15, binary
                  cls
clus                 0   1
  ZNF483 MUTATED     0   3
  ZNF483 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF483 MUTATED      0    3
  ZNF483 WILD-TYPE    5  102
                        clus
vv                       ZNF483 MUTATED ZNF483 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(177) Variable = ANKRD28 MUTATION ANALYSIS
D177V1, survival
                   sevent
clus2                0  1
  ANKRD28 MUTATED    1  5
  ANKRD28 WILD-TYPE 67 71
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
                6               138 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
                5                71 
$`ANKRD28 MUTATED`
TCGA-3A-A9IC TCGA-FB-AAQ3 TCGA-HZ-7919 TCGA-IB-7651 TCGA-IB-8127 TCGA-XD-AAUI 
       24.26         1.02        19.50        19.82        17.16        12.03 

$`ANKRD28 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        42.31        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        58.98        43.50        20.84         7.36        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         7.50        12.53 
TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 TCGA-FB-AAQ1 TCGA-FB-AAQ2 TCGA-H6-8124 
       34.82        23.54        15.55         4.04         5.03        12.89 
TCGA-H6-A45N TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       30.25        17.49         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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-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-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        24.23        17.26        23.08        22.85        39.98 
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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
             1.02              0.03 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
            24.26             75.12 
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
           18.330            14.155 
[1] "1.0 - 24.3 (18.3)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.5"
D177V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ANKRD28 MUTATED          0        0         0         6         0        0
  ANKRD28 WILD-TYPE        3        8        23        97         4        4
D177V3, multiclass
           clus
vv          ANKRD28 MUTATED ANKRD28 WILD-TYPE
  STAGE IA                0                 3
  STAGE IB                0                 8
  STAGE IIA               0                23
  STAGE IIB               6                97
  STAGE III               0                 4
  STAGE IV                0                 4
[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
  ANKRD28 MUTATED     0   0     6
  ANKRD28 WILD-TYPE   4  16   119
D177V4, multiclass
       clus
vv      ANKRD28 MUTATED ANKRD28 WILD-TYPE
  T1                  0                 4
  T2                  0                16
  T3+T4               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"
D177V5, binary
                   cls
clus                  0   1
  ANKRD28 MUTATED     0   6
  ANKRD28 WILD-TYPE  37 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED      0    6
  ANKRD28 WILD-TYPE   37  102
   clus
vv  ANKRD28 MUTATED ANKRD28 WILD-TYPE
  0               0                37
  1               6               102
[1] 2 2
[1] FALSE
D177V6, binary
                   cls
clus                 0  1
  ANKRD28 MUTATED    3  0
  ANKRD28 WILD-TYPE 63  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED      3    0
  ANKRD28 WILD-TYPE   63    4
   clus
vv  ANKRD28 MUTATED ANKRD28 WILD-TYPE
  0               3                63
  1               0                 4
[1] 2 2
[1] FALSE
D177V7, binary
                   cls
clus                 0  1
  ANKRD28 MUTATED    5  1
  ANKRD28 WILD-TYPE 62 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED      5    1
  ANKRD28 WILD-TYPE   62   78
        clus
vv       ANKRD28 MUTATED ANKRD28 WILD-TYPE
  FEMALE               5                62
  MALE                 1                78
[1] 2 2
[1] FALSE
D177V8, binary
                   cls
clus                 0  1
  ANKRD28 MUTATED    4  1
  ANKRD28 WILD-TYPE 90 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED      4    1
  ANKRD28 WILD-TYPE   90   35
     clus
vv    ANKRD28 MUTATED ANKRD28 WILD-TYPE
  NO                4                90
  YES               1                35
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANKRD28 MUTATED                                     6
  ANKRD28 WILD-TYPE                                 124
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANKRD28 MUTATED                                       0
  ANKRD28 WILD-TYPE                                    13
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANKRD28 MUTATED                                                  0
  ANKRD28 WILD-TYPE                                                2
D177V9, multiclass
                                                  clus
vv                                                 ANKRD28 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 ANKRD28 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           13
  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"
D177V10, continuous
[1] "Remove cluster labels:" "ANKRD28 MUTATED"       
clus
  ANKRD28 MUTATED ANKRD28 WILD-TYPE 
                2                48 
       TCGA-2J-AAB1        TCGA-2J-AABA        TCGA-2J-AABE        TCGA-2J-AABF 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-2J-AABO        TCGA-2J-AABV        TCGA-2L-AAQA        TCGA-2L-AAQE 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-3A-A9I9        TCGA-3A-A9IB        TCGA-3A-A9IX        TCGA-F2-A8YN 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-FB-A4P5        TCGA-FB-A4P6        TCGA-FB-A5VM        TCGA-FB-A78T 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-FB-AAPS        TCGA-FB-AAPY        TCGA-H6-8124        TCGA-H6-A45N 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-HV-AA8V        TCGA-HZ-A77Q        TCGA-HZ-A8P0        TCGA-HZ-A8P1 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7885        TCGA-IB-7886 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126        TCGA-IB-A5SS 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-IB-A6UF        TCGA-IB-A6UG        TCGA-IB-A7M4        TCGA-IB-AAUQ 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-IB-AAUS        TCGA-IB-AAUT        TCGA-IB-AAUU        TCGA-LB-A7SX 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-LB-A9Q5        TCGA-OE-A75W        TCGA-S4-A8RM        TCGA-S4-A8RP 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
       TCGA-US-A774        TCGA-XD-AAUL        TCGA-XN-A8T5        TCGA-YY-A8LH 
"ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" "ANKRD28 WILD-TYPE" 
D177V11, continuous
                   vv
clus                R0 R1 R2 RX
  ANKRD28 MUTATED    3  3  0  0
  ANKRD28 WILD-TYPE 76 47  4  3
D177V12, multiclass
    clus
vv   ANKRD28 MUTATED ANKRD28 WILD-TYPE
  R0               3                76
  R1               3                47
  R2               0                 4
  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"
D177V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANKRD28 MUTATED       0                         0     6
  ANKRD28 WILD-TYPE     9                         5   122
D177V14, multiclass
                           clus
vv                          ANKRD28 MUTATED ANKRD28 WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               0                 5
  WHITE                                   6               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"
D177V15, binary
                   cls
clus                 0  1
  ANKRD28 MUTATED    0  6
  ANKRD28 WILD-TYPE  5 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD28 MUTATED      0    6
  ANKRD28 WILD-TYPE    5   99
                        clus
vv                       ANKRD28 MUTATED ANKRD28 WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               6                99
[1] 2 2
[1] FALSE

Clustering(178) Variable = DIO1 MUTATION ANALYSIS
D178V1, survival
                sevent
clus2             0  1
  DIO1 MUTATED    1  3
  DIO1 WILD-TYPE 67 73
  DIO1 MUTATED DIO1 WILD-TYPE 
             4            140 
  DIO1 MUTATED DIO1 WILD-TYPE 
             3             73 
$`DIO1 MUTATED`
TCGA-HZ-7925 TCGA-HZ-A77Q TCGA-IB-7887 TCGA-PZ-A5RE 
       20.19         1.08         3.62        15.45 

$`DIO1 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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        1.02        12.89        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 
       66.94         8.28        30.25        17.49        19.50         0.13 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 TCGA-HZ-8315 
       17.03        23.21        12.03        19.59         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-HZ-A9TJ 
        6.38        21.60         5.26        10.85         0.23        19.82 
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-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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-Q3-A5QY TCGA-Q3-AA2A 
       12.46        10.29        19.20         8.78        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH 
       39.98        16.80        14.14         0.39        13.81        12.99 
TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.03        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  DIO1 MUTATED DIO1 WILD-TYPE 
          1.08           0.03 
  DIO1 MUTATED DIO1 WILD-TYPE 
         20.19          75.12 
  DIO1 MUTATED DIO1 WILD-TYPE 
         9.535         14.285 
[1] "1.1 - 20.2 (9.5)"  "0.0 - 75.1 (14.3)"
[1] "hr=" "2.3"
D178V2, continuous
                vv
clus             STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  DIO1 MUTATED          0        0         0         4         0        0
  DIO1 WILD-TYPE        3        8        23        99         4        4
D178V3, multiclass
           clus
vv          DIO1 MUTATED DIO1 WILD-TYPE
  STAGE IA             0              3
  STAGE IB             0              8
  STAGE IIA            0             23
  STAGE IIB            4             99
  STAGE III            0              4
  STAGE IV             0              4
[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
  DIO1 MUTATED     0   0     4
  DIO1 WILD-TYPE   4  16   121
D178V4, multiclass
       clus
vv      DIO1 MUTATED DIO1 WILD-TYPE
  T1               0              4
  T2               0             16
  T3+T4            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"
D178V5, binary
                cls
clus               0   1
  DIO1 MUTATED     0   4
  DIO1 WILD-TYPE  37 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  DIO1 MUTATED      0    4
  DIO1 WILD-TYPE   37  104
   clus
vv  DIO1 MUTATED DIO1 WILD-TYPE
  0            0             37
  1            4            104
[1] 2 2
[1] FALSE
D178V6, binary
                cls
clus              0  1
  DIO1 MUTATED    1  0
  DIO1 WILD-TYPE 65  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DIO1 MUTATED      1    0
  DIO1 WILD-TYPE   65    4
   clus
vv  DIO1 MUTATED DIO1 WILD-TYPE
  0            1             65
  1            0              4
[1] 2 2
[1] FALSE
D178V7, binary
                cls
clus              0  1
  DIO1 MUTATED    3  1
  DIO1 WILD-TYPE 64 78
[1] "tbl2"
                cls
clus             [,1] [,2]
  DIO1 MUTATED      3    1
  DIO1 WILD-TYPE   64   78
        clus
vv       DIO1 MUTATED DIO1 WILD-TYPE
  FEMALE            3             64
  MALE              1             78
[1] 2 2
[1] FALSE
D178V8, binary
                cls
clus              0  1
  DIO1 MUTATED    2  1
  DIO1 WILD-TYPE 92 35
[1] "tbl2"
                cls
clus             [,1] [,2]
  DIO1 MUTATED      2    1
  DIO1 WILD-TYPE   92   35
     clus
vv    DIO1 MUTATED DIO1 WILD-TYPE
  NO             2             92
  YES            1             35
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DIO1 MUTATED                                     3
  DIO1 WILD-TYPE                                 127
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DIO1 MUTATED                                       1
  DIO1 WILD-TYPE                                    12
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DIO1 MUTATED                                                  0
  DIO1 WILD-TYPE                                                2
D178V9, multiclass
                                                  clus
vv                                                 DIO1 MUTATED DIO1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3            127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1             12
  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"
D178V10, continuous
[1] "Remove cluster labels:" "DIO1 MUTATED"          
clus
  DIO1 MUTATED DIO1 WILD-TYPE 
             2             48 
    TCGA-2J-AAB1     TCGA-2J-AABA     TCGA-2J-AABE     TCGA-2J-AABF 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-2J-AABO     TCGA-2J-AABV     TCGA-2L-AAQA     TCGA-2L-AAQE 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-3A-A9I9     TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-F2-A8YN 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-FB-A4P5     TCGA-FB-A4P6     TCGA-FB-A5VM     TCGA-FB-A78T 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-FB-AAPS     TCGA-FB-AAPY     TCGA-H6-8124     TCGA-H6-A45N 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-HV-AA8V     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-IB-AAUU     TCGA-LB-A7SX 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-LB-A9Q5     TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-S4-A8RP 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-US-A774     TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
D178V11, continuous
[1] "Remove cluster labels:" "DIO1 MUTATED"          
clus
  DIO1 MUTATED DIO1 WILD-TYPE 
             1             39 
    TCGA-2J-AAB1     TCGA-2J-AABE     TCGA-2J-AABF     TCGA-2J-AABO 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-3A-A9IB     TCGA-3A-A9IX     TCGA-FB-A4P5     TCGA-FB-A4P6 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-AAPS     TCGA-FB-AAPY 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-H6-8124     TCGA-HZ-A8P0     TCGA-HZ-A8P1     TCGA-IB-7644 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-IB-7649     TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-7886 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-IB-7891     TCGA-IB-8126     TCGA-IB-8127     TCGA-IB-A5SS 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-IB-A6UF     TCGA-IB-A6UG     TCGA-IB-A7M4     TCGA-IB-AAUQ 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-IB-AAUS     TCGA-IB-AAUT     TCGA-LB-A7SX     TCGA-LB-A9Q5 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-OE-A75W     TCGA-S4-A8RM     TCGA-US-A774     TCGA-XD-AAUI 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
    TCGA-XD-AAUL     TCGA-XN-A8T5     TCGA-YY-A8LH 
"DIO1 WILD-TYPE" "DIO1 WILD-TYPE" "DIO1 WILD-TYPE" 
                vv
clus             R0 R1 R2 RX
  DIO1 MUTATED    2  1  0  0
  DIO1 WILD-TYPE 77 49  4  3
D178V12, multiclass
    clus
vv   DIO1 MUTATED DIO1 WILD-TYPE
  R0            2             77
  R1            1             49
  R2            0              4
  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"
D178V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DIO1 MUTATED       0                         0     4
  DIO1 WILD-TYPE     9                         5   124
D178V14, multiclass
                           clus
vv                          DIO1 MUTATED DIO1 WILD-TYPE
  ASIAN                                0              9
  BLACK OR AFRICAN AMERICAN            0              5
  WHITE                                4            124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V15, binary
                cls
clus               0   1
  DIO1 MUTATED     0   4
  DIO1 WILD-TYPE   5 101
[1] "tbl2"
                cls
clus             [,1] [,2]
  DIO1 MUTATED      0    4
  DIO1 WILD-TYPE    5  101
                        clus
vv                       DIO1 MUTATED DIO1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            4            101
[1] 2 2
[1] FALSE

Clustering(179) Variable = KLK15 MUTATION ANALYSIS
D179V1, survival
                 sevent
clus2              0  1
  KLK15 MUTATED    2  3
  KLK15 WILD-TYPE 66 73
  KLK15 MUTATED KLK15 WILD-TYPE 
              5             139 
  KLK15 MUTATED KLK15 WILD-TYPE 
              3              73 
$`KLK15 MUTATED`
TCGA-2J-AAB9 TCGA-3A-A9I5 TCGA-3A-A9J0 TCGA-IB-7651 TCGA-IB-A6UG 
       20.61        58.98        24.43        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        42.31        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 
       43.50        20.84         7.36        24.26        33.57        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        12.66 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ 
       16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 
        5.26        10.85         1.08         0.23        19.82        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-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-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 
        9.40        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  KLK15 MUTATED KLK15 WILD-TYPE 
           1.35            0.03 
  KLK15 MUTATED KLK15 WILD-TYPE 
          58.98           75.12 
  KLK15 MUTATED KLK15 WILD-TYPE 
          20.61           14.14 
[1] "1.4 - 59.0 (20.6)" "0.0 - 75.1 (14.1)"
[1] "hr=" "1.4"
D179V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KLK15 MUTATED          0        0         0         4         0        0
  KLK15 WILD-TYPE        3        8        23        99         4        4
D179V3, multiclass
           clus
vv          KLK15 MUTATED KLK15 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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     0   0     4
  KLK15 WILD-TYPE   4  16   121
D179V4, multiclass
       clus
vv      KLK15 MUTATED KLK15 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D179V5, binary
                 cls
clus                0   1
  KLK15 MUTATED     1   4
  KLK15 WILD-TYPE  36 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      1    4
  KLK15 WILD-TYPE   36  104
   clus
vv  KLK15 MUTATED KLK15 WILD-TYPE
  0             1              36
  1             4             104
[1] 2 2
[1] FALSE
D179V6, binary
                 cls
clus               0  1
  KLK15 MUTATED    3  0
  KLK15 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      3    0
  KLK15 WILD-TYPE   63    4
   clus
vv  KLK15 MUTATED KLK15 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D179V7, binary
                 cls
clus               0  1
  KLK15 MUTATED    2  3
  KLK15 WILD-TYPE 65 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      2    3
  KLK15 WILD-TYPE   65   76
        clus
vv       KLK15 MUTATED KLK15 WILD-TYPE
  FEMALE             2              65
  MALE               3              76
[1] 2 2
[1] FALSE
D179V8, binary
                 cls
clus               0  1
  KLK15 MUTATED    3  2
  KLK15 WILD-TYPE 91 34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      3    2
  KLK15 WILD-TYPE   91   34
     clus
vv    KLK15 MUTATED KLK15 WILD-TYPE
  NO              3              91
  YES             2              34
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KLK15 MUTATED                                     5
  KLK15 WILD-TYPE                                 125
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KLK15 MUTATED                                       0
  KLK15 WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KLK15 MUTATED                                                  0
  KLK15 WILD-TYPE                                                2
D179V9, 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                          125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D179V10, continuous
[1] "Remove cluster labels:" "KLK15 MUTATED"         
clus
  KLK15 MUTATED KLK15 WILD-TYPE 
              2              48 
     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-HV-AA8V      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-7887      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
D179V11, continuous
[1] "Remove cluster labels:" "KLK15 MUTATED"         
clus
  KLK15 MUTATED KLK15 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"KLK15 WILD-TYPE" "KLK15 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  KLK15 MUTATED    4  1  0  0
  KLK15 WILD-TYPE 75 49  4  3
D179V12, multiclass
    clus
vv   KLK15 MUTATED KLK15 WILD-TYPE
  R0             4              75
  R1             1              49
  R2             0               4
  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"
D179V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLK15 MUTATED       0                         0     5
  KLK15 WILD-TYPE     9                         5   123
D179V14, multiclass
                           clus
vv                          KLK15 MUTATED KLK15 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D179V15, binary
                 cls
clus                0   1
  KLK15 MUTATED     0   4
  KLK15 WILD-TYPE   5 101
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK15 MUTATED      0    4
  KLK15 WILD-TYPE    5  101
                        clus
vv                       KLK15 MUTATED KLK15 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             4             101
[1] 2 2
[1] FALSE

Clustering(180) Variable = BOC MUTATION ANALYSIS
D180V1, survival
               sevent
clus2            0  1
  BOC MUTATED    1  3
  BOC WILD-TYPE 67 73
  BOC MUTATED BOC WILD-TYPE 
            4           140 
  BOC MUTATED BOC WILD-TYPE 
            3            73 
$`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        42.31        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        58.98        43.50        20.84         7.36        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-A9TJ 
        6.38        21.60         5.26        10.85         1.08        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY 
       12.99        16.37        31.27        23.67        11.51        12.76 
TCGA-YY-A8LH TCGA-Z5-AAPL 
       66.28        15.35 

  BOC MUTATED BOC WILD-TYPE 
         0.23          0.03 
  BOC MUTATED BOC WILD-TYPE 
        24.26         75.12 
  BOC MUTATED BOC WILD-TYPE 
       15.925        14.285 
[1] "0.2 - 24.3 (15.9)" "0.0 - 75.1 (14.3)"
[1] "hr=" "1.4"
D180V2, 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        3        7        23       100         4        4
D180V3, multiclass
           clus
vv          BOC MUTATED BOC WILD-TYPE
  STAGE IA            0             3
  STAGE IB            1             7
  STAGE IIA           0            23
  STAGE IIB           3           100
  STAGE III           0             4
  STAGE IV            0             4
[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   4  15   122
D180V4, multiclass
       clus
vv      BOC MUTATED BOC WILD-TYPE
  T1              0             4
  T2              1            15
  T3+T4           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"
D180V5, binary
               cls
clus              0   1
  BOC MUTATED     1   3
  BOC WILD-TYPE  36 105
[1] "tbl2"
               cls
clus            [,1] [,2]
  BOC MUTATED      1    3
  BOC WILD-TYPE   36  105
   clus
vv  BOC MUTATED BOC WILD-TYPE
  0           1            36
  1           3           105
[1] 2 2
[1] FALSE
D180V6, binary
               cls
clus             0  1
  BOC MUTATED    1  0
  BOC WILD-TYPE 65  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  BOC MUTATED      1    0
  BOC WILD-TYPE   65    4
   clus
vv  BOC MUTATED BOC WILD-TYPE
  0           1            65
  1           0             4
[1] 2 2
[1] FALSE
D180V7, binary
               cls
clus             0  1
  BOC MUTATED    3  1
  BOC WILD-TYPE 64 78
[1] "tbl2"
               cls
clus            [,1] [,2]
  BOC MUTATED      3    1
  BOC WILD-TYPE   64   78
        clus
vv       BOC MUTATED BOC WILD-TYPE
  FEMALE           3            64
  MALE             1            78
[1] 2 2
[1] FALSE
D180V8, binary
               cls
clus             0  1
  BOC MUTATED    2  1
  BOC WILD-TYPE 92 35
[1] "tbl2"
               cls
clus            [,1] [,2]
  BOC MUTATED      2    1
  BOC WILD-TYPE   92   35
     clus
vv    BOC MUTATED BOC WILD-TYPE
  NO            2            92
  YES           1            35
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BOC MUTATED                                     4
  BOC WILD-TYPE                                 126
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BOC MUTATED                                       0
  BOC WILD-TYPE                                    13
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BOC MUTATED                                                  0
  BOC WILD-TYPE                                                2
D180V9, multiclass
                                                  clus
vv                                                 BOC MUTATED BOC WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4           126
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0            13
  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"
D180V10, continuous
[1] "Remove cluster labels:" "BOC MUTATED"           
clus
  BOC MUTATED BOC WILD-TYPE 
            2            48 
   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-HV-AA8V    TCGA-HZ-A77Q    TCGA-HZ-A8P0    TCGA-IB-7644    TCGA-IB-7649 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-IB-7885    TCGA-IB-7886    TCGA-IB-7887    TCGA-IB-7891    TCGA-IB-8126 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-IB-8127    TCGA-IB-A5SS    TCGA-IB-A6UF    TCGA-IB-A6UG    TCGA-IB-A7M4 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-IB-AAUQ    TCGA-IB-AAUS    TCGA-IB-AAUT    TCGA-IB-AAUU    TCGA-LB-A7SX 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-LB-A9Q5    TCGA-OE-A75W    TCGA-S4-A8RM    TCGA-S4-A8RP    TCGA-US-A774 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
   TCGA-XD-AAUL    TCGA-XN-A8T5    TCGA-YY-A8LH 
"BOC WILD-TYPE" "BOC WILD-TYPE" "BOC WILD-TYPE" 
D180V11, continuous
               vv
clus            R0 R1 R2 RX
  BOC MUTATED    3  1  0  0
  BOC WILD-TYPE 76 49  4  3
D180V12, multiclass
    clus
vv   BOC MUTATED BOC WILD-TYPE
  R0           3            76
  R1           1            49
  R2           0             4
  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"
D180V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BOC MUTATED       0                         0     4
  BOC WILD-TYPE     9                         5   124
D180V14, multiclass
                           clus
vv                          BOC MUTATED BOC WILD-TYPE
  ASIAN                               0             9
  BLACK OR AFRICAN AMERICAN           0             5
  WHITE                               4           124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V15, binary
               cls
clus              0   1
  BOC MUTATED     0   4
  BOC WILD-TYPE   5 101
[1] "tbl2"
               cls
clus            [,1] [,2]
  BOC MUTATED      0    4
  BOC WILD-TYPE    5  101
                        clus
vv                       BOC MUTATED BOC WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO           4           101
[1] 2 2
[1] FALSE

Clustering(181) Variable = NDUFV2 MUTATION ANALYSIS
D181V1, survival
                  sevent
clus2               0  1
  NDUFV2 MUTATED    3  0
  NDUFV2 WILD-TYPE 65 76
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              141 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               0               76 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        12.95        49.38         4.77        21.90        15.35 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 TCGA-IB-7888 
       19.82        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        24.23 
TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G 
       23.08        22.85        39.98        16.80        14.14         0.39 
TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 
       13.81        12.99        12.03        16.37        31.27        23.67 
TCGA-YB-A89D TCGA-YH-A8SY TCGA-Z5-AAPL 
       11.51        12.76        15.35 

  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           17.00             0.03 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           66.28            75.12 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           17.26            14.14 
[1] "17.0 - 66.3 (17.3)" "0.0 - 75.1 (14.1)" 
[1] "hr="     "2.6e+07"
D181V2, 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        3        8        22       101         4        4
D181V3, multiclass
           clus
vv          NDUFV2 MUTATED NDUFV2 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              1               22
  STAGE IIB              2              101
  STAGE III              0                4
  STAGE IV               0                4
[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   4  16   122
D181V4, multiclass
       clus
vv      NDUFV2 MUTATED NDUFV2 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D181V5, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     1   2
  NDUFV2 WILD-TYPE  36 106
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    2
  NDUFV2 WILD-TYPE   36  106
   clus
vv  NDUFV2 MUTATED NDUFV2 WILD-TYPE
  0              1               36
  1              2              106
[1] 2 2
[1] FALSE
D181V6, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    1  0
  NDUFV2 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    0
  NDUFV2 WILD-TYPE   65    4
   clus
vv  NDUFV2 MUTATED NDUFV2 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D181V7, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    2  1
  NDUFV2 WILD-TYPE 65 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      2    1
  NDUFV2 WILD-TYPE   65   78
        clus
vv       NDUFV2 MUTATED NDUFV2 WILD-TYPE
  FEMALE              2               65
  MALE                1               78
[1] 2 2
[1] FALSE
D181V8, binary
                  cls
clus                0  1
  NDUFV2 MUTATED    1  2
  NDUFV2 WILD-TYPE 93 34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    2
  NDUFV2 WILD-TYPE   93   34
     clus
vv    NDUFV2 MUTATED NDUFV2 WILD-TYPE
  NO               1               93
  YES              2               34
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NDUFV2 MUTATED                                     3
  NDUFV2 WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NDUFV2 MUTATED                                       0
  NDUFV2 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NDUFV2 MUTATED                                                  0
  NDUFV2 WILD-TYPE                                                2
D181V9, 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                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D181V10, continuous
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
clus
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               2               48 
      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-HV-AA8V 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1       TCGA-IB-7644 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-7649       TCGA-IB-7651       TCGA-IB-7885       TCGA-IB-7886 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-IB-7887       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-IB-AAUU 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-S4-A8RP       TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
D181V11, continuous
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
clus
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               1               39 
      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       TCGA-XN-A8T5 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  NDUFV2 MUTATED    1  2  0  0
  NDUFV2 WILD-TYPE 78 48  4  3
D181V12, multiclass
    clus
vv   NDUFV2 MUTATED NDUFV2 WILD-TYPE
  R0              1               78
  R1              2               48
  R2              0                4
  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"
D181V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NDUFV2 MUTATED       0                         0     3
  NDUFV2 WILD-TYPE     9                         5   125
D181V14, multiclass
                           clus
vv                          NDUFV2 MUTATED NDUFV2 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V15, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     0   3
  NDUFV2 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      0    3
  NDUFV2 WILD-TYPE    5  102
                        clus
vv                       NDUFV2 MUTATED NDUFV2 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(182) Variable = MAP3K9 MUTATION ANALYSIS
D182V1, survival
                  sevent
clus2               0  1
  MAP3K9 MUTATED    2  3
  MAP3K9 WILD-TYPE 66 73
  MAP3K9 MUTATED MAP3K9 WILD-TYPE 
               5              139 
  MAP3K9 MUTATED MAP3K9 WILD-TYPE 
               3               73 
$`MAP3K9 MUTATED`
TCGA-2L-AAQL TCGA-3A-A9I9 TCGA-IB-7651 TCGA-IB-A5SP TCGA-IB-AAUU 
        9.60        20.84        19.82        15.85         8.05 

$`MAP3K9 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        42.31        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-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU 
       58.98        43.50         7.36        24.26        33.57        15.06 
TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 
       34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-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-LB-A7SX TCGA-LB-A8F3 TCGA-LB-A9Q5 
       11.11         7.40         9.44        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        24.23        17.26        23.08        22.85        39.98 
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-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  MAP3K9 MUTATED MAP3K9 WILD-TYPE 
            8.05             0.03 
  MAP3K9 MUTATED MAP3K9 WILD-TYPE 
           20.84            75.12 
  MAP3K9 MUTATED MAP3K9 WILD-TYPE 
           15.85            14.17 
[1] "8.1 - 20.8 (15.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.2"
D182V2, continuous
                  vv
clus               STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MAP3K9 MUTATED          0        0         2         3         0        0
  MAP3K9 WILD-TYPE        3        8        21       100         4        4
D182V3, multiclass
           clus
vv          MAP3K9 MUTATED MAP3K9 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              2               21
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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
  MAP3K9 MUTATED     0   0     5
  MAP3K9 WILD-TYPE   4  16   120
D182V4, multiclass
       clus
vv      MAP3K9 MUTATED MAP3K9 WILD-TYPE
  T1                 0                4
  T2                 0               16
  T3+T4              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"
D182V5, binary
                  cls
clus                 0   1
  MAP3K9 MUTATED     2   3
  MAP3K9 WILD-TYPE  35 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K9 MUTATED      2    3
  MAP3K9 WILD-TYPE   35  105
   clus
vv  MAP3K9 MUTATED MAP3K9 WILD-TYPE
  0              2               35
  1              3              105
[1] 2 2
[1] FALSE
D182V6, binary
                  cls
clus                0  1
  MAP3K9 MUTATED    3  0
  MAP3K9 WILD-TYPE 63  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K9 MUTATED      3    0
  MAP3K9 WILD-TYPE   63    4
   clus
vv  MAP3K9 MUTATED MAP3K9 WILD-TYPE
  0              3               63
  1              0                4
[1] 2 2
[1] FALSE
D182V7, binary
                  cls
clus                0  1
  MAP3K9 MUTATED    1  4
  MAP3K9 WILD-TYPE 66 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K9 MUTATED      1    4
  MAP3K9 WILD-TYPE   66   75
        clus
vv       MAP3K9 MUTATED MAP3K9 WILD-TYPE
  FEMALE              1               66
  MALE                4               75
[1] 2 2
[1] FALSE
D182V8, binary
                  cls
clus                0  1
  MAP3K9 MUTATED    4  1
  MAP3K9 WILD-TYPE 90 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K9 MUTATED      4    1
  MAP3K9 WILD-TYPE   90   35
     clus
vv    MAP3K9 MUTATED MAP3K9 WILD-TYPE
  NO               4               90
  YES              1               35
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAP3K9 MUTATED                                     5
  MAP3K9 WILD-TYPE                                 125
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAP3K9 MUTATED                                       0
  MAP3K9 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAP3K9 MUTATED                                                  0
  MAP3K9 WILD-TYPE                                                2
D182V9, multiclass
                                                  clus
vv                                                 MAP3K9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 MAP3K9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           125
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D182V10, continuous
D182V11, continuous
[1] "Remove cluster labels:" "MAP3K9 MUTATED"        
clus
  MAP3K9 MUTATED MAP3K9 WILD-TYPE 
               1               39 
      TCGA-2J-AAB1       TCGA-2J-AABE       TCGA-2J-AABF       TCGA-2J-AABO 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
      TCGA-3A-A9IB       TCGA-3A-A9IX       TCGA-FB-A4P5       TCGA-FB-A4P6 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-AAPS       TCGA-FB-AAPY 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
      TCGA-H6-8124       TCGA-HZ-A77Q       TCGA-HZ-A8P0       TCGA-HZ-A8P1 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
      TCGA-IB-7644       TCGA-IB-7649       TCGA-IB-7885       TCGA-IB-7886 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-LB-A7SX       TCGA-LB-A9Q5 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
      TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-US-A774       TCGA-XD-AAUI 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
      TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" "MAP3K9 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  MAP3K9 MUTATED    3  1  0  1
  MAP3K9 WILD-TYPE 76 49  4  2
D182V12, multiclass
    clus
vv   MAP3K9 MUTATED MAP3K9 WILD-TYPE
  R0              3               76
  R1              1               49
  R2              0                4
  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"
D182V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP3K9 MUTATED       0                         0     5
  MAP3K9 WILD-TYPE     9                         5   123
D182V14, multiclass
                           clus
vv                          MAP3K9 MUTATED MAP3K9 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              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"
D182V15, binary
                  cls
clus                 0   1
  MAP3K9 MUTATED     0   3
  MAP3K9 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K9 MUTATED      0    3
  MAP3K9 WILD-TYPE    5  102
                        clus
vv                       MAP3K9 MUTATED MAP3K9 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(183) Variable = TNRC6C MUTATION ANALYSIS
D183V1, survival
                  sevent
clus2               0  1
  TNRC6C MUTATED    3  3
  TNRC6C WILD-TYPE 65 73
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               6              138 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               3               73 
$`TNRC6C MUTATED`
TCGA-2J-AABR TCGA-FB-A78T TCGA-FB-AAPU TCGA-HZ-8317 TCGA-IB-7651 TCGA-RB-AA9M 
       14.40         0.03        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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ 
       15.06        34.09        10.13        24.43        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        12.66        16.37         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V 
        4.21         7.63         9.50        66.94         8.28        30.25 
TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
       17.49        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 
       10.85         1.08         0.23        19.82        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-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 
       24.23        17.26        23.08        22.85        39.98        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        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  TNRC6C MUTATED TNRC6C WILD-TYPE 
            0.03             0.13 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           19.82            75.12 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           12.48            14.70 
[1] "0.0 - 19.8 (12.5)" "0.1 - 75.1 (14.7)"
[1] "hr=" "1.5"
D183V2, 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        3        8        21        99         4        4
D183V3, multiclass
           clus
vv          TNRC6C MUTATED TNRC6C WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              2               21
  STAGE IIB              4               99
  STAGE III              0                4
  STAGE IV               0                4
[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   3  16   120
D183V4, multiclass
       clus
vv      TNRC6C MUTATED TNRC6C WILD-TYPE
  T1                 1                3
  T2                 0               16
  T3+T4              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"
D183V5, binary
                  cls
clus                 0   1
  TNRC6C MUTATED     2   4
  TNRC6C WILD-TYPE  35 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      2    4
  TNRC6C WILD-TYPE   35  104
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0              2               35
  1              4              104
[1] 2 2
[1] FALSE
D183V6, binary
                  cls
clus                0  1
  TNRC6C MUTATED    3  0
  TNRC6C WILD-TYPE 63  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      3    0
  TNRC6C WILD-TYPE   63    4
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0              3               63
  1              0                4
[1] 2 2
[1] FALSE
D183V7, binary
                  cls
clus                0  1
  TNRC6C MUTATED    5  1
  TNRC6C WILD-TYPE 62 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      5    1
  TNRC6C WILD-TYPE   62   78
        clus
vv       TNRC6C MUTATED TNRC6C WILD-TYPE
  FEMALE              5               62
  MALE                1               78
[1] 2 2
[1] FALSE
D183V8, binary
                  cls
clus                0  1
  TNRC6C MUTATED    3  2
  TNRC6C WILD-TYPE 91 34
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      3    2
  TNRC6C WILD-TYPE   91   34
     clus
vv    TNRC6C MUTATED TNRC6C WILD-TYPE
  NO               3               91
  YES              2               34
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TNRC6C MUTATED                                     6
  TNRC6C WILD-TYPE                                 124
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TNRC6C MUTATED                                       0
  TNRC6C WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TNRC6C MUTATED                                                  0
  TNRC6C WILD-TYPE                                                2
D183V9, 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                           124
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D183V10, continuous
[1] "Remove cluster labels:" "TNRC6C MUTATED"        
clus
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               2               48 
      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-HV-AA8V 
"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-7887 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127       TCGA-IB-A5SS 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4       TCGA-IB-AAUQ 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU       TCGA-LB-A7SX 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM       TCGA-S4-A8RP 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
      TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5       TCGA-YY-A8LH 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
D183V11, continuous
[1] "Remove cluster labels:" "TNRC6C MUTATED"        
clus
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               2               38 
      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-XN-A8T5       TCGA-YY-A8LH 
"TNRC6C WILD-TYPE" "TNRC6C WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  TNRC6C MUTATED    4  2  0  0
  TNRC6C WILD-TYPE 75 48  4  3
D183V12, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  R0              4               75
  R1              2               48
  R2              0                4
  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"
D183V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNRC6C MUTATED       1                         0     5
  TNRC6C WILD-TYPE     8                         5   123
D183V14, multiclass
                           clus
vv                          TNRC6C MUTATED TNRC6C WILD-TYPE
  ASIAN                                  1                8
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  5              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"
D183V15, binary
                  cls
clus                 0   1
  TNRC6C MUTATED     0   5
  TNRC6C WILD-TYPE   5 100
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED      0    5
  TNRC6C WILD-TYPE    5  100
                        clus
vv                       TNRC6C MUTATED TNRC6C WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              5              100
[1] 2 2
[1] FALSE

Clustering(184) Variable = PDXDC1 MUTATION ANALYSIS
D184V1, survival
                  sevent
clus2               0  1
  PDXDC1 MUTATED    1  2
  PDXDC1 WILD-TYPE 67 74
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               3              141 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               2               74 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-A7B8 TCGA-RB-AA9M TCGA-S4-A8RM TCGA-S4-A8RO TCGA-S4-A8RP 
        3.12        15.32         9.40        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
            1.02             0.03 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
           23.54            75.12 
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
           19.82            14.17 
[1] "1.0 - 23.5 (19.8)" "0.0 - 75.1 (14.2)"
[1] "hr=" "1.1"
D184V2, 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        3        8        23       100         4        4
D184V3, multiclass
           clus
vv          PDXDC1 MUTATED PDXDC1 WILD-TYPE
  STAGE IA               0                3
  STAGE IB               0                8
  STAGE IIA              0               23
  STAGE IIB              3              100
  STAGE III              0                4
  STAGE IV               0                4
[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   4  15   123
D184V4, multiclass
       clus
vv      PDXDC1 MUTATED PDXDC1 WILD-TYPE
  T1                 0                4
  T2                 1               15
  T3+T4              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"
D184V5, binary
                  cls
clus                 0   1
  PDXDC1 MUTATED     0   3
  PDXDC1 WILD-TYPE  37 105
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      0    3
  PDXDC1 WILD-TYPE   37  105
   clus
vv  PDXDC1 MUTATED PDXDC1 WILD-TYPE
  0              0               37
  1              3              105
[1] 2 2
[1] FALSE
D184V6, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    1  0
  PDXDC1 WILD-TYPE 65  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      1    0
  PDXDC1 WILD-TYPE   65    4
   clus
vv  PDXDC1 MUTATED PDXDC1 WILD-TYPE
  0              1               65
  1              0                4
[1] 2 2
[1] FALSE
D184V7, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    2  1
  PDXDC1 WILD-TYPE 65 78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      2    1
  PDXDC1 WILD-TYPE   65   78
        clus
vv       PDXDC1 MUTATED PDXDC1 WILD-TYPE
  FEMALE              2               65
  MALE                1               78
[1] 2 2
[1] FALSE
D184V8, binary
                  cls
clus                0  1
  PDXDC1 MUTATED    3  0
  PDXDC1 WILD-TYPE 91 36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      3    0
  PDXDC1 WILD-TYPE   91   36
     clus
vv    PDXDC1 MUTATED PDXDC1 WILD-TYPE
  NO               3               91
  YES              0               36
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDXDC1 MUTATED                                     3
  PDXDC1 WILD-TYPE                                 127
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDXDC1 MUTATED                                       0
  PDXDC1 WILD-TYPE                                    13
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDXDC1 MUTATED                                                  0
  PDXDC1 WILD-TYPE                                                2
D184V9, 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                           127
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          13
  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"
D184V10, continuous
[1] "Remove cluster labels:" "PDXDC1 MUTATED"        
clus
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               1               49 
      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-HV-AA8V       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-7887       TCGA-IB-7891       TCGA-IB-8126       TCGA-IB-8127 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-A5SS       TCGA-IB-A6UF       TCGA-IB-A6UG       TCGA-IB-A7M4 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-IB-AAUQ       TCGA-IB-AAUS       TCGA-IB-AAUT       TCGA-IB-AAUU 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-LB-A9Q5       TCGA-OE-A75W       TCGA-S4-A8RM 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-S4-A8RP       TCGA-US-A774       TCGA-XD-AAUL       TCGA-XN-A8T5 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
      TCGA-YY-A8LH 
"PDXDC1 WILD-TYPE" 
D184V11, continuous
[1] "Remove cluster labels:" "PDXDC1 MUTATED"        
clus
  PDXDC1 MUTATED PDXDC1 WILD-TYPE 
               1               39 
      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-XN-A8T5       TCGA-YY-A8LH 
"PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" "PDXDC1 WILD-TYPE" 
                  vv
clus               R0 R1 R2 RX
  PDXDC1 MUTATED    3  0  0  0
  PDXDC1 WILD-TYPE 76 50  4  3
D184V12, multiclass
    clus
vv   PDXDC1 MUTATED PDXDC1 WILD-TYPE
  R0              3               76
  R1              0               50
  R2              0                4
  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"
D184V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDXDC1 MUTATED       0                         0     3
  PDXDC1 WILD-TYPE     9                         5   125
D184V14, multiclass
                           clus
vv                          PDXDC1 MUTATED PDXDC1 WILD-TYPE
  ASIAN                                  0                9
  BLACK OR AFRICAN AMERICAN              0                5
  WHITE                                  3              125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V15, binary
                  cls
clus                 0   1
  PDXDC1 MUTATED     0   3
  PDXDC1 WILD-TYPE   5 102
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDXDC1 MUTATED      0    3
  PDXDC1 WILD-TYPE    5  102
                        clus
vv                       PDXDC1 MUTATED PDXDC1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              3              102
[1] 2 2
[1] FALSE

Clustering(185) Variable = MIPEP MUTATION ANALYSIS
D185V1, survival
                 sevent
clus2              0  1
  MIPEP MUTATED    0  3
  MIPEP WILD-TYPE 68 73
  MIPEP MUTATED MIPEP WILD-TYPE 
              3             141 
  MIPEP MUTATED MIPEP WILD-TYPE 
              3              73 
$`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        42.31        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        58.98        43.50        20.84         7.36        24.26 
TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY 
       33.57        15.06        34.09        10.13        24.43        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        12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 
       12.89        13.84         4.21         7.63         9.50        66.94 
TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 
        8.28        30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-7888 TCGA-IB-7889 TCGA-IB-7890 
       23.80        41.33         4.04        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        24.23        17.26        23.08 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG 
       22.85        39.98        16.80        14.14         0.39        13.81 
TCGA-XD-AAUH TCGA-XD-AAUI TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D 
       12.99        12.03        16.37        31.27        23.67        11.51 
TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       12.76        66.28        15.35 

  MIPEP MUTATED MIPEP WILD-TYPE 
           3.62            0.03 
  MIPEP MUTATED MIPEP WILD-TYPE 
          10.98           75.12 
  MIPEP MUTATED MIPEP WILD-TYPE 
           3.95           14.47 
[1] "3.6 - 11.0 (4.0)"  "0.0 - 75.1 (14.5)"
[1] "hr=" "8.2"
D185V2, 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        3        8        23       100         4        4
D185V3, multiclass
           clus
vv          MIPEP MUTATED MIPEP WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             0              23
  STAGE IIB             3             100
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   122
D185V4, multiclass
       clus
vv      MIPEP MUTATED MIPEP WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D185V5, binary
                 cls
clus                0   1
  MIPEP MUTATED     0   3
  MIPEP WILD-TYPE  37 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      0    3
  MIPEP WILD-TYPE   37  105
   clus
vv  MIPEP MUTATED MIPEP WILD-TYPE
  0             0              37
  1             3             105
[1] 2 2
[1] FALSE
D185V6, binary
                 cls
clus               0  1
  MIPEP MUTATED    2  0
  MIPEP WILD-TYPE 64  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      2    0
  MIPEP WILD-TYPE   64    4
   clus
vv  MIPEP MUTATED MIPEP WILD-TYPE
  0             2              64
  1             0               4
[1] 2 2
[1] FALSE
D185V7, binary
                 cls
clus               0  1
  MIPEP MUTATED    1  2
  MIPEP WILD-TYPE 66 77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      1    2
  MIPEP WILD-TYPE   66   77
        clus
vv       MIPEP MUTATED MIPEP WILD-TYPE
  FEMALE             1              66
  MALE               2              77
[1] 2 2
[1] FALSE
D185V8, binary
                 cls
clus               0  1
  MIPEP MUTATED    3  0
  MIPEP WILD-TYPE 91 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      3    0
  MIPEP WILD-TYPE   91   36
     clus
vv    MIPEP MUTATED MIPEP WILD-TYPE
  NO              3              91
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MIPEP MUTATED                                     2
  MIPEP WILD-TYPE                                 128
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MIPEP MUTATED                                       1
  MIPEP WILD-TYPE                                    12
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MIPEP MUTATED                                                  0
  MIPEP WILD-TYPE                                                2
D185V9, 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                          128
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         12
  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"
D185V10, continuous
[1] "Remove cluster labels:" "MIPEP MUTATED"         
clus
  MIPEP MUTATED MIPEP WILD-TYPE 
              1              49 
     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-HV-AA8V      TCGA-HZ-A77Q      TCGA-HZ-A8P0      TCGA-HZ-A8P1 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-IB-7644      TCGA-IB-7649      TCGA-IB-7651      TCGA-IB-7885 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-IB-7886      TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-IB-A5SS      TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-IB-AAUQ      TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-S4-A8RP      TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5 
"MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" "MIPEP WILD-TYPE" 
     TCGA-YY-A8LH 
"MIPEP WILD-TYPE" 
D185V11, continuous
                 vv
clus              R0 R1 R2 RX
  MIPEP MUTATED    1  2  0  0
  MIPEP WILD-TYPE 78 48  4  3
D185V12, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  R0             1              78
  R1             2              48
  R2             0               4
  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"
D185V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MIPEP MUTATED       0                         0     3
  MIPEP WILD-TYPE     9                         5   125
D185V14, multiclass
                           clus
vv                          MIPEP MUTATED MIPEP WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 3             125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V15, binary
                 cls
clus                0   1
  MIPEP MUTATED     0   2
  MIPEP WILD-TYPE   5 103
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      0    2
  MIPEP WILD-TYPE    5  103
                        clus
vv                       MIPEP MUTATED MIPEP WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             2             103
[1] 2 2
[1] FALSE

Clustering(186) Variable = ENPP7 MUTATION ANALYSIS
D186V1, survival
                 sevent
clus2              0  1
  ENPP7 MUTATED    0  5
  ENPP7 WILD-TYPE 68 71
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              5             139 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              5              71 
$`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        42.31        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 
       58.98        43.50        20.84         7.36        24.26        33.57 
TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-F2-6879 
       15.06        34.09        10.13        24.43        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 
       12.66        16.37         0.03         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-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 TCGA-HV-A5A6 TCGA-HV-A7OL 
       13.84         4.21         7.63         9.50        66.94         8.28 
TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-7926 
       30.25        17.49        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        19.59         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-HZ-A9TJ 
       21.60         5.26        10.85         1.08         0.23        19.82 
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-AAUP TCGA-IB-AAUQ 
        8.22        15.88         0.26         4.73        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        24.23        17.26        23.08        22.85 
TCGA-US-A776 TCGA-US-A779 TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUH TCGA-XD-AAUI 
       39.98        16.80         0.39        13.81        12.99        12.03 
TCGA-XD-AAUL TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH 
       16.37        31.27        23.67        11.51        12.76        66.28 
TCGA-Z5-AAPL 
       15.35 

  ENPP7 MUTATED ENPP7 WILD-TYPE 
           2.17            0.03 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
          71.74           75.12 
  ENPP7 MUTATED ENPP7 WILD-TYPE 
          14.14           14.40 
[1] "2.2 - 71.7 (14.1)" "0.0 - 75.1 (14.4)"
[1] "hr=" "1.4"
D186V2, 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        3        8        22        99         4        4
D186V3, multiclass
           clus
vv          ENPP7 MUTATED ENPP7 WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB             4              99
  STAGE III             0               4
  STAGE IV              0               4
[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   4  16   120
D186V4, multiclass
       clus
vv      ENPP7 MUTATED ENPP7 WILD-TYPE
  T1                0               4
  T2                0              16
  T3+T4             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"
D186V5, binary
                 cls
clus                0   1
  ENPP7 MUTATED     1   4
  ENPP7 WILD-TYPE  36 104
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      1    4
  ENPP7 WILD-TYPE   36  104
   clus
vv  ENPP7 MUTATED ENPP7 WILD-TYPE
  0             1              36
  1             4             104
[1] 2 2
[1] FALSE
D186V6, binary
                 cls
clus               0  1
  ENPP7 MUTATED    3  0
  ENPP7 WILD-TYPE 63  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      3    0
  ENPP7 WILD-TYPE   63    4
   clus
vv  ENPP7 MUTATED ENPP7 WILD-TYPE
  0             3              63
  1             0               4
[1] 2 2
[1] FALSE
D186V7, binary
                 cls
clus               0  1
  ENPP7 MUTATED    2  3
  ENPP7 WILD-TYPE 65 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      2    3
  ENPP7 WILD-TYPE   65   76
        clus
vv       ENPP7 MUTATED ENPP7 WILD-TYPE
  FEMALE             2              65
  MALE               3              76
[1] 2 2
[1] FALSE
D186V8, binary
                 cls
clus               0  1
  ENPP7 MUTATED    4  0
  ENPP7 WILD-TYPE 90 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      4    0
  ENPP7 WILD-TYPE   90   36
     clus
vv    ENPP7 MUTATED ENPP7 WILD-TYPE
  NO              4              90
  YES             0              36
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ENPP7 MUTATED                                     3
  ENPP7 WILD-TYPE                                 127
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ENPP7 MUTATED                                       2
  ENPP7 WILD-TYPE                                    11
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ENPP7 MUTATED                                                  0
  ENPP7 WILD-TYPE                                                2
D186V9, 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                          127
  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"
D186V10, continuous
[1] "Remove cluster labels:" "ENPP7 MUTATED"         
clus
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              2              48 
     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-HV-AA8V 
"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-7887 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-7891      TCGA-IB-8126      TCGA-IB-8127      TCGA-IB-A5SS 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-A6UF      TCGA-IB-A6UG      TCGA-IB-A7M4      TCGA-IB-AAUQ 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-IB-AAUS      TCGA-IB-AAUT      TCGA-IB-AAUU      TCGA-LB-A7SX 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-LB-A9Q5      TCGA-OE-A75W      TCGA-S4-A8RM      TCGA-S4-A8RP 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
     TCGA-US-A774      TCGA-XD-AAUL      TCGA-XN-A8T5      TCGA-YY-A8LH 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
D186V11, continuous
[1] "Remove cluster labels:" "ENPP7 MUTATED"         
clus
  ENPP7 MUTATED ENPP7 WILD-TYPE 
              2              38 
     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-XN-A8T5      TCGA-YY-A8LH 
"ENPP7 WILD-TYPE" "ENPP7 WILD-TYPE" 
                 vv
clus              R0 R1 R2 RX
  ENPP7 MUTATED    2  2  0  0
  ENPP7 WILD-TYPE 77 48  4  3
D186V12, multiclass
    clus
vv   ENPP7 MUTATED ENPP7 WILD-TYPE
  R0             2              77
  R1             2              48
  R2             0               4
  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"
D186V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ENPP7 MUTATED       0                         0     5
  ENPP7 WILD-TYPE     9                         5   123
D186V14, multiclass
                           clus
vv                          ENPP7 MUTATED ENPP7 WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                 5             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"
D186V15, binary
                 cls
clus                0   1
  ENPP7 MUTATED     1   3
  ENPP7 WILD-TYPE   4 102
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP7 MUTATED      1    3
  ENPP7 WILD-TYPE    4  102
                        clus
vv                       ENPP7 MUTATED ENPP7 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             3             102
[1] 2 2
[1] FALSE

Clustering(187) Variable = FCGBP MUTATION ANALYSIS
D187V1, survival
                 sevent
clus2              0  1
  FCGBP MUTATED    5  7
  FCGBP WILD-TYPE 63 69
  FCGBP MUTATED FCGBP WILD-TYPE 
             12             132 
  FCGBP MUTATED FCGBP WILD-TYPE 
              7              69 
$`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        58.98         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        42.31        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        43.50        20.84 
TCGA-3A-A9IB TCGA-3A-A9IC TCGA-3A-A9IH TCGA-3A-A9IU TCGA-3A-A9IX TCGA-3A-A9IZ 
        7.36        24.26        33.57        15.06        34.09        10.13 
TCGA-3A-A9J0 TCGA-3E-AAAY TCGA-3E-AAAZ TCGA-F2-6879 TCGA-F2-A44G TCGA-F2-A44H 
       24.43        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        12.66        16.37 
TCGA-FB-A78T TCGA-FB-AAPS TCGA-FB-AAPU TCGA-FB-AAPY TCGA-FB-AAPZ TCGA-FB-AAQ0 
        0.03         7.50        12.53        34.82        23.54        15.55 
TCGA-FB-AAQ2 TCGA-FB-AAQ3 TCGA-H6-A45N TCGA-HV-A5A3 TCGA-HV-A5A4 TCGA-HV-A5A5 
        5.03         1.02        13.84         4.21         7.63         9.50 
TCGA-HV-A5A6 TCGA-HV-A7OL TCGA-HV-AA8V TCGA-HV-AA8X TCGA-HZ-7919 TCGA-HZ-7925 
       66.94         8.28        30.25        17.49        19.50        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        19.59         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-HZ-A9TJ TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 TCGA-IB-7649 
       19.82        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-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-AAUN TCGA-IB-AAUO TCGA-IB-AAUP TCGA-IB-AAUR 
        8.22        15.88         4.73         7.86        14.17        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        24.23        17.26        23.08        22.85        39.98 
TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-XD-AAUG TCGA-XD-AAUI TCGA-XD-AAUL 
       16.80        14.14         0.39        13.81        12.03        16.37 
TCGA-XN-A8T3 TCGA-XN-A8T5 TCGA-YB-A89D TCGA-YH-A8SY TCGA-YY-A8LH TCGA-Z5-AAPL 
       31.27        23.67        11.51        12.76        66.28        15.35 

  FCGBP MUTATED FCGBP WILD-TYPE 
           0.13            0.03 
  FCGBP MUTATED FCGBP WILD-TYPE 
          58.98           75.12 
  FCGBP MUTATED FCGBP WILD-TYPE 
          9.615          15.090 
[1] "0.1 - 59.0 (9.6)"  "0.0 - 75.1 (15.1)"
[1] "hr=" "1.9"
D187V2, continuous
                 vv
clus              STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FCGBP MUTATED          0        0         1        10         0        0
  FCGBP WILD-TYPE        3        8        22        93         4        4
D187V3, multiclass
           clus
vv          FCGBP MUTATED FCGBP WILD-TYPE
  STAGE IA              0               3
  STAGE IB              0               8
  STAGE IIA             1              22
  STAGE IIB            10              93
  STAGE III             0               4
  STAGE IV              0               4
[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     0   1    10
  FCGBP WILD-TYPE   4  15   115
D187V4, multiclass
       clus
vv      FCGBP MUTATED FCGBP WILD-TYPE
  T1                0               4
  T2                1              15
  T3+T4            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"
D187V5, binary
                 cls
clus               0  1
  FCGBP MUTATED    2 10
  FCGBP WILD-TYPE 35 98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      2   10
  FCGBP WILD-TYPE   35   98
   clus
vv  FCGBP MUTATED FCGBP WILD-TYPE
  0             2              35
  1            10              98
[1] 2 2
[1] FALSE
D187V6, binary
                 cls
clus               0  1
  FCGBP MUTATED    7  0
  FCGBP WILD-TYPE 59  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      7    0
  FCGBP WILD-TYPE   59    4
   clus
vv  FCGBP MUTATED FCGBP WILD-TYPE
  0             7              59
  1             0               4
[1] 2 2
[1] FALSE
D187V7, binary
                 cls
clus               0  1
  FCGBP MUTATED    4  8
  FCGBP WILD-TYPE 63 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      4    8
  FCGBP WILD-TYPE   63   71
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  FEMALE             4              63
  MALE               8              71
[1] 2 2
[1] FALSE
D187V8, binary
                 cls
clus               0  1
  FCGBP MUTATED    8  3
  FCGBP WILD-TYPE 86 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      8    3
  FCGBP WILD-TYPE   86   33
     clus
vv    FCGBP MUTATED FCGBP WILD-TYPE
  NO              8              86
  YES             3              33
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FCGBP MUTATED                                    12
  FCGBP WILD-TYPE                                 118
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FCGBP MUTATED                                       0
  FCGBP WILD-TYPE                                    13
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FCGBP MUTATED                                                  0
  FCGBP WILD-TYPE                                                2
D187V9, 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                          118
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         13
  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"
D187V10, continuous
D187V11, continuous
                 vv
clus              R0 R1 R2 RX
  FCGBP MUTATED    7  3  1  1
  FCGBP WILD-TYPE 72 47  3  2
D187V12, multiclass
    clus
vv   FCGBP MUTATED FCGBP WILD-TYPE
  R0             7              72
  R1             3              47
  R2             1               3
  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"
D187V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FCGBP MUTATED       0                         0    12
  FCGBP WILD-TYPE     9                         5   116
D187V14, multiclass
                           clus
vv                          FCGBP MUTATED FCGBP WILD-TYPE
  ASIAN                                 0               9
  BLACK OR AFRICAN AMERICAN             0               5
  WHITE                                12             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"
D187V15, binary
                 cls
clus               0  1
  FCGBP MUTATED    0  8
  FCGBP WILD-TYPE  5 97
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      0    8
  FCGBP WILD-TYPE    5   97
                        clus
vv                       FCGBP MUTATED FCGBP WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             8              97
[1] 2 2
[1] FALSE
