[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-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/10006103/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/10686733/transformed.cor.cli.txt"

nPatients in clinical file=93, in cluster file=41, common to both=33
[1] "Reduce the number of clustering variables from 174 to 130."
[1] 130  33
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            22             11 
  KRAS MUTATED KRAS WILD-TYPE 
            22             11 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            18             15 
  TP53 MUTATED TP53 WILD-TYPE 
            18             15 
[1] "C19ORF55 MUTATION ANALYSIS"
[1] 3
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                 7                 26 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                 7                 26 
[1] "B4GALT2 MUTATION ANALYSIS"
[1] 3
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
                5                28 
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
                5                28 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               6               27 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               6               27 
[1] "NFIL3 MUTATION ANALYSIS"
[1] 3
  NFIL3 MUTATED NFIL3 WILD-TYPE 
              6              27 
  NFIL3 MUTATED NFIL3 WILD-TYPE 
              6              27 
[1] "OTOF MUTATION ANALYSIS"
[1] 3
  OTOF MUTATED OTOF WILD-TYPE 
             7             26 
  OTOF MUTATED OTOF WILD-TYPE 
             7             26 
[1] "IRS1 MUTATION ANALYSIS"
[1] 3
  IRS1 MUTATED IRS1 WILD-TYPE 
             6             27 
  IRS1 MUTATED IRS1 WILD-TYPE 
             6             27 
[1] "GAS2L2 MUTATION ANALYSIS"
[1] 3
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               5               28 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               5               28 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              5              28 
  RBM10 MUTATED RBM10 WILD-TYPE 
              5              28 
[1] "APP MUTATION ANALYSIS"
[1] 3
  APP MUTATED APP WILD-TYPE 
            6            27 
  APP MUTATED APP WILD-TYPE 
            6            27 
[1] "IPP MUTATION ANALYSIS"
[1] 3
  IPP MUTATED IPP WILD-TYPE 
            4            29 
  IPP MUTATED IPP WILD-TYPE 
            4            29 
[1] "MAMLD1 MUTATION ANALYSIS"
[1] 3
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               7               26 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               7               26 
[1] "ARHGAP18 MUTATION ANALYSIS"
[1] 3
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 3                 30 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 3                 30 
[1] "PHF8 MUTATION ANALYSIS"
[1] 3
  PHF8 MUTATED PHF8 WILD-TYPE 
             4             29 
  PHF8 MUTATED PHF8 WILD-TYPE 
             4             29 
[1] "THBS4 MUTATION ANALYSIS"
[1] 3
  THBS4 MUTATED THBS4 WILD-TYPE 
              6              27 
  THBS4 MUTATED THBS4 WILD-TYPE 
              6              27 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7              26 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7              26 
[1] "PTPRF MUTATION ANALYSIS"
[1] 3
  PTPRF MUTATED PTPRF WILD-TYPE 
              6              27 
  PTPRF MUTATED PTPRF WILD-TYPE 
              6              27 
[1] "MED12 MUTATION ANALYSIS"
[1] 3
  MED12 MUTATED MED12 WILD-TYPE 
              5              28 
  MED12 MUTATED MED12 WILD-TYPE 
              5              28 
[1] "BMP2K MUTATION ANALYSIS"
[1] 3
  BMP2K MUTATED BMP2K WILD-TYPE 
              3              30 
  BMP2K MUTATED BMP2K WILD-TYPE 
              3              30 
[1] "ZMYM5 MUTATION ANALYSIS"
[1] 3
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
              4              29 
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
              4              29 
[1] "SYT15 MUTATION ANALYSIS"
[1] 3
  SYT15 MUTATED SYT15 WILD-TYPE 
              3              30 
  SYT15 MUTATED SYT15 WILD-TYPE 
              3              30 
[1] "PLAU MUTATION ANALYSIS"
[1] 3
  PLAU MUTATED PLAU WILD-TYPE 
             4             29 
  PLAU MUTATED PLAU WILD-TYPE 
             4             29 
[1] "MEPCE MUTATION ANALYSIS"
[1] 3
  MEPCE MUTATED MEPCE WILD-TYPE 
              3              30 
  MEPCE MUTATED MEPCE WILD-TYPE 
              3              30 
[1] "ZMIZ1 MUTATION ANALYSIS"
[1] 3
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              5              28 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              5              28 
[1] "SLC39A5 MUTATION ANALYSIS"
[1] 3
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
                4                29 
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
                4                29 
[1] "GUCY2F MUTATION ANALYSIS"
[1] 3
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               5               28 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               5               28 
[1] "EDC4 MUTATION ANALYSIS"
[1] 3
  EDC4 MUTATED EDC4 WILD-TYPE 
             5             28 
  EDC4 MUTATED EDC4 WILD-TYPE 
             5             28 
[1] "SEH1L MUTATION ANALYSIS"
[1] 3
  SEH1L MUTATED SEH1L WILD-TYPE 
              3              30 
  SEH1L MUTATED SEH1L WILD-TYPE 
              3              30 
[1] "SLC4A3 MUTATION ANALYSIS"
[1] 3
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               3               30 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               3               30 
[1] "CD99L2 MUTATION ANALYSIS"
[1] 3
  CD99L2 MUTATED CD99L2 WILD-TYPE 
               3               30 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
               3               30 
[1] "SBNO1 MUTATION ANALYSIS"
[1] 3
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              3              30 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              3              30 
[1] "NPNT MUTATION ANALYSIS"
[1] 3
  NPNT MUTATED NPNT WILD-TYPE 
             3             30 
  NPNT MUTATED NPNT WILD-TYPE 
             3             30 
[1] "TMEM175 MUTATION ANALYSIS"
[1] 3
  TMEM175 MUTATED TMEM175 WILD-TYPE 
                4                29 
  TMEM175 MUTATED TMEM175 WILD-TYPE 
                4                29 
[1] "IRX4 MUTATION ANALYSIS"
[1] 3
  IRX4 MUTATED IRX4 WILD-TYPE 
             3             30 
  IRX4 MUTATED IRX4 WILD-TYPE 
             3             30 
[1] "CLCC1 MUTATION ANALYSIS"
[1] 3
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              3              30 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              3              30 
[1] "BTNL8 MUTATION ANALYSIS"
[1] 3
  BTNL8 MUTATED BTNL8 WILD-TYPE 
              4              29 
  BTNL8 MUTATED BTNL8 WILD-TYPE 
              4              29 
[1] "SYNGAP1 MUTATION ANALYSIS"
[1] 3
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
                4                29 
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
                4                29 
[1] "F8 MUTATION ANALYSIS"
[1] 3
  F8 MUTATED F8 WILD-TYPE 
           3           30 
  F8 MUTATED F8 WILD-TYPE 
           3           30 
[1] "SORBS2 MUTATION ANALYSIS"
[1] 3
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               4               29 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               4               29 
[1] "NR4A3 MUTATION ANALYSIS"
[1] 3
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              3              30 
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              3              30 
[1] "ZNF337 MUTATION ANALYSIS"
[1] 3
  ZNF337 MUTATED ZNF337 WILD-TYPE 
               4               29 
  ZNF337 MUTATED ZNF337 WILD-TYPE 
               4               29 
[1] "TAOK2 MUTATION ANALYSIS"
[1] 3
  TAOK2 MUTATED TAOK2 WILD-TYPE 
              4              29 
  TAOK2 MUTATED TAOK2 WILD-TYPE 
              4              29 
[1] "UNC5A MUTATION ANALYSIS"
[1] 3
  UNC5A MUTATED UNC5A WILD-TYPE 
              3              30 
  UNC5A MUTATED UNC5A WILD-TYPE 
              3              30 
[1] "TNFSF9 MUTATION ANALYSIS"
[1] 3
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
               4               29 
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
               4               29 
[1] "TEX2 MUTATION ANALYSIS"
[1] 3
  TEX2 MUTATED TEX2 WILD-TYPE 
             4             29 
  TEX2 MUTATED TEX2 WILD-TYPE 
             4             29 
[1] "RBM43 MUTATION ANALYSIS"
[1] 3
  RBM43 MUTATED RBM43 WILD-TYPE 
              3              30 
  RBM43 MUTATED RBM43 WILD-TYPE 
              3              30 
[1] "CIR1 MUTATION ANALYSIS"
[1] 3
  CIR1 MUTATED CIR1 WILD-TYPE 
             3             30 
  CIR1 MUTATED CIR1 WILD-TYPE 
             3             30 
[1] "TOX4 MUTATION ANALYSIS"
[1] 3
  TOX4 MUTATED TOX4 WILD-TYPE 
             4             29 
  TOX4 MUTATED TOX4 WILD-TYPE 
             4             29 
[1] "HIBCH MUTATION ANALYSIS"
[1] 3
  HIBCH MUTATED HIBCH WILD-TYPE 
              3              30 
  HIBCH MUTATED HIBCH WILD-TYPE 
              3              30 
[1] "CRAT MUTATION ANALYSIS"
[1] 3
  CRAT MUTATED CRAT WILD-TYPE 
             3             30 
  CRAT MUTATED CRAT WILD-TYPE 
             3             30 
[1] "SRP14 MUTATION ANALYSIS"
[1] 3
  SRP14 MUTATED SRP14 WILD-TYPE 
              3              30 
  SRP14 MUTATED SRP14 WILD-TYPE 
              3              30 
[1] "PDZD7 MUTATION ANALYSIS"
[1] 3
  PDZD7 MUTATED PDZD7 WILD-TYPE 
              3              30 
  PDZD7 MUTATED PDZD7 WILD-TYPE 
              3              30 
[1] "POP5 MUTATION ANALYSIS"
[1] 3
  POP5 MUTATED POP5 WILD-TYPE 
             3             30 
  POP5 MUTATED POP5 WILD-TYPE 
             3             30 
[1] "UNC5D MUTATION ANALYSIS"
[1] 3
  UNC5D MUTATED UNC5D WILD-TYPE 
              3              30 
  UNC5D MUTATED UNC5D WILD-TYPE 
              3              30 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
               5               28 
  FAM47C MUTATED FAM47C WILD-TYPE 
               5               28 
[1] "TMEM184A MUTATION ANALYSIS"
[1] 3
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 4                 29 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 4                 29 
[1] "BEGAIN MUTATION ANALYSIS"
[1] 3
  BEGAIN MUTATED BEGAIN WILD-TYPE 
               4               29 
  BEGAIN MUTATED BEGAIN WILD-TYPE 
               4               29 
[1] "PASD1 MUTATION ANALYSIS"
[1] 3
  PASD1 MUTATED PASD1 WILD-TYPE 
              5              28 
  PASD1 MUTATED PASD1 WILD-TYPE 
              5              28 
[1] "RBM45 MUTATION ANALYSIS"
[1] 3
  RBM45 MUTATED RBM45 WILD-TYPE 
              4              29 
  RBM45 MUTATED RBM45 WILD-TYPE 
              4              29 
[1] "POM121 MUTATION ANALYSIS"
[1] 3
  POM121 MUTATED POM121 WILD-TYPE 
               4               29 
  POM121 MUTATED POM121 WILD-TYPE 
               4               29 
[1] "EME2 MUTATION ANALYSIS"
[1] 3
  EME2 MUTATED EME2 WILD-TYPE 
             3             30 
  EME2 MUTATED EME2 WILD-TYPE 
             3             30 
[1] "CUL4B MUTATION ANALYSIS"
[1] 3
  CUL4B MUTATED CUL4B WILD-TYPE 
              3              30 
  CUL4B MUTATED CUL4B WILD-TYPE 
              3              30 
[1] "IFT46 MUTATION ANALYSIS"
[1] 3
  IFT46 MUTATED IFT46 WILD-TYPE 
              4              29 
  IFT46 MUTATED IFT46 WILD-TYPE 
              4              29 
[1] "OTUD4 MUTATION ANALYSIS"
[1] 3
  OTUD4 MUTATED OTUD4 WILD-TYPE 
              5              28 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
              5              28 
[1] "GABBR1 MUTATION ANALYSIS"
[1] 3
  GABBR1 MUTATED GABBR1 WILD-TYPE 
               4               29 
  GABBR1 MUTATED GABBR1 WILD-TYPE 
               4               29 
[1] "MYH10 MUTATION ANALYSIS"
[1] 3
  MYH10 MUTATED MYH10 WILD-TYPE 
              4              29 
  MYH10 MUTATED MYH10 WILD-TYPE 
              4              29 
[1] "ERF MUTATION ANALYSIS"
[1] 3
  ERF MUTATED ERF WILD-TYPE 
            4            29 
  ERF MUTATED ERF WILD-TYPE 
            4            29 
[1] "OR10A7 MUTATION ANALYSIS"
[1] 3
  OR10A7 MUTATED OR10A7 WILD-TYPE 
               3               30 
  OR10A7 MUTATED OR10A7 WILD-TYPE 
               3               30 
[1] "BRDT MUTATION ANALYSIS"
[1] 3
  BRDT MUTATED BRDT WILD-TYPE 
             4             29 
  BRDT MUTATED BRDT WILD-TYPE 
             4             29 
[1] "CDHR5 MUTATION ANALYSIS"
[1] 3
  CDHR5 MUTATED CDHR5 WILD-TYPE 
              4              29 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
              4              29 
[1] "GPR25 MUTATION ANALYSIS"
[1] 3
  GPR25 MUTATED GPR25 WILD-TYPE 
              3              30 
  GPR25 MUTATED GPR25 WILD-TYPE 
              3              30 
[1] "PPARGC1B MUTATION ANALYSIS"
[1] 3
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 3                 30 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 3                 30 
[1] "SALL1 MUTATION ANALYSIS"
[1] 3
  SALL1 MUTATED SALL1 WILD-TYPE 
              4              29 
  SALL1 MUTATED SALL1 WILD-TYPE 
              4              29 
[1] "VEPH1 MUTATION ANALYSIS"
[1] 3
  VEPH1 MUTATED VEPH1 WILD-TYPE 
              4              29 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
              4              29 
[1] "ST6GALNAC5 MUTATION ANALYSIS"
[1] 3
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                   3                   30 
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                   3                   30 
[1] "MST1 MUTATION ANALYSIS"
[1] 3
  MST1 MUTATED MST1 WILD-TYPE 
             5             28 
  MST1 MUTATED MST1 WILD-TYPE 
             5             28 
[1] "GRB7 MUTATION ANALYSIS"
[1] 3
  GRB7 MUTATED GRB7 WILD-TYPE 
             4             29 
  GRB7 MUTATED GRB7 WILD-TYPE 
             4             29 
[1] "TMC4 MUTATION ANALYSIS"
[1] 3
  TMC4 MUTATED TMC4 WILD-TYPE 
             4             29 
  TMC4 MUTATED TMC4 WILD-TYPE 
             4             29 
[1] "MED9 MUTATION ANALYSIS"
[1] 3
  MED9 MUTATED MED9 WILD-TYPE 
             3             30 
  MED9 MUTATED MED9 WILD-TYPE 
             3             30 
[1] "WASF3 MUTATION ANALYSIS"
[1] 3
  WASF3 MUTATED WASF3 WILD-TYPE 
              3              30 
  WASF3 MUTATED WASF3 WILD-TYPE 
              3              30 
[1] "GIT1 MUTATION ANALYSIS"
[1] 3
  GIT1 MUTATED GIT1 WILD-TYPE 
             3             30 
  GIT1 MUTATED GIT1 WILD-TYPE 
             3             30 
[1] "UGP2 MUTATION ANALYSIS"
[1] 3
  UGP2 MUTATED UGP2 WILD-TYPE 
             4             29 
  UGP2 MUTATED UGP2 WILD-TYPE 
             4             29 
[1] "ERCC3 MUTATION ANALYSIS"
[1] 3
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              3              30 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              3              30 
[1] "HMX2 MUTATION ANALYSIS"
[1] 3
  HMX2 MUTATED HMX2 WILD-TYPE 
             3             30 
  HMX2 MUTATED HMX2 WILD-TYPE 
             3             30 
[1] "AARS2 MUTATION ANALYSIS"
[1] 3
  AARS2 MUTATED AARS2 WILD-TYPE 
              4              29 
  AARS2 MUTATED AARS2 WILD-TYPE 
              4              29 
[1] "ALS2CR11 MUTATION ANALYSIS"
[1] 3
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
                 3                 30 
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
                 3                 30 
[1] "ARFGAP3 MUTATION ANALYSIS"
[1] 3
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                3                30 
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                3                30 
[1] "CHGA MUTATION ANALYSIS"
[1] 3
  CHGA MUTATED CHGA WILD-TYPE 
             3             30 
  CHGA MUTATED CHGA WILD-TYPE 
             3             30 
[1] "FAM63B MUTATION ANALYSIS"
[1] 3
  FAM63B MUTATED FAM63B WILD-TYPE 
               3               30 
  FAM63B MUTATED FAM63B WILD-TYPE 
               3               30 
[1] "VPS36 MUTATION ANALYSIS"
[1] 3
  VPS36 MUTATED VPS36 WILD-TYPE 
              3              30 
  VPS36 MUTATED VPS36 WILD-TYPE 
              3              30 
[1] "MAP3K7 MUTATION ANALYSIS"
[1] 3
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               3               30 
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               3               30 
[1] "OTX1 MUTATION ANALYSIS"
[1] 3
  OTX1 MUTATED OTX1 WILD-TYPE 
             4             29 
  OTX1 MUTATED OTX1 WILD-TYPE 
             4             29 
[1] "NFAT5 MUTATION ANALYSIS"
[1] 3
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              3              30 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              3              30 
[1] "WHSC1L1 MUTATION ANALYSIS"
[1] 3
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                3                30 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                3                30 
[1] "KIAA1211 MUTATION ANALYSIS"
[1] 3
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 3                 30 
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 3                 30 
[1] "PPIG MUTATION ANALYSIS"
[1] 3
  PPIG MUTATED PPIG WILD-TYPE 
             3             30 
  PPIG MUTATED PPIG WILD-TYPE 
             3             30 
[1] "SLITRK5 MUTATION ANALYSIS"
[1] 3
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
                3                30 
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
                3                30 
[1] "MBD3 MUTATION ANALYSIS"
[1] 3
  MBD3 MUTATED MBD3 WILD-TYPE 
             3             30 
  MBD3 MUTATED MBD3 WILD-TYPE 
             3             30 
[1] "FOXP2 MUTATION ANALYSIS"
[1] 3
  FOXP2 MUTATED FOXP2 WILD-TYPE 
              4              29 
  FOXP2 MUTATED FOXP2 WILD-TYPE 
              4              29 
[1] "NAPSA MUTATION ANALYSIS"
[1] 3
  NAPSA MUTATED NAPSA WILD-TYPE 
              3              30 
  NAPSA MUTATED NAPSA WILD-TYPE 
              3              30 
[1] "EIF3C MUTATION ANALYSIS"
[1] 3
  EIF3C MUTATED EIF3C WILD-TYPE 
              3              30 
  EIF3C MUTATED EIF3C WILD-TYPE 
              3              30 
[1] "GTF2F1 MUTATION ANALYSIS"
[1] 3
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               3               30 
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               3               30 
[1] "CCKAR MUTATION ANALYSIS"
[1] 3
  CCKAR MUTATED CCKAR WILD-TYPE 
              3              30 
  CCKAR MUTATED CCKAR WILD-TYPE 
              3              30 
[1] "MMP14 MUTATION ANALYSIS"
[1] 3
  MMP14 MUTATED MMP14 WILD-TYPE 
              3              30 
  MMP14 MUTATED MMP14 WILD-TYPE 
              3              30 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
            3            30 
  ATM MUTATED ATM WILD-TYPE 
            3            30 
[1] "IFFO1 MUTATION ANALYSIS"
[1] 3
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              3              30 
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              3              30 
[1] "TWISTNB MUTATION ANALYSIS"
[1] 3
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                3                30 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                3                30 
[1] "SPAG9 MUTATION ANALYSIS"
[1] 3
  SPAG9 MUTATED SPAG9 WILD-TYPE 
              3              30 
  SPAG9 MUTATED SPAG9 WILD-TYPE 
              3              30 
[1] "SMCR7 MUTATION ANALYSIS"
[1] 3
  SMCR7 MUTATED SMCR7 WILD-TYPE 
              3              30 
  SMCR7 MUTATED SMCR7 WILD-TYPE 
              3              30 
[1] "PSAT1 MUTATION ANALYSIS"
[1] 3
  PSAT1 MUTATED PSAT1 WILD-TYPE 
              3              30 
  PSAT1 MUTATED PSAT1 WILD-TYPE 
              3              30 
[1] "PDILT MUTATION ANALYSIS"
[1] 3
  PDILT MUTATED PDILT WILD-TYPE 
              3              30 
  PDILT MUTATED PDILT WILD-TYPE 
              3              30 
[1] "CCDC8 MUTATION ANALYSIS"
[1] 3
  CCDC8 MUTATED CCDC8 WILD-TYPE 
              3              30 
  CCDC8 MUTATED CCDC8 WILD-TYPE 
              3              30 
[1] "HIST1H2BK MUTATION ANALYSIS"
[1] 3
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  3                  30 
  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE 
                  3                  30 
[1] "SCRIB MUTATION ANALYSIS"
[1] 3
  SCRIB MUTATED SCRIB WILD-TYPE 
              3              30 
  SCRIB MUTATED SCRIB WILD-TYPE 
              3              30 
[1] "STAU1 MUTATION ANALYSIS"
[1] 3
  STAU1 MUTATED STAU1 WILD-TYPE 
              3              30 
  STAU1 MUTATED STAU1 WILD-TYPE 
              3              30 
[1] "GOLGA6B MUTATION ANALYSIS"
[1] 3
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                3                30 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                3                30 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
             3             30 
  IRS4 MUTATED IRS4 WILD-TYPE 
             3             30 
[1] "PDZD2 MUTATION ANALYSIS"
[1] 3
  PDZD2 MUTATED PDZD2 WILD-TYPE 
              4              29 
  PDZD2 MUTATED PDZD2 WILD-TYPE 
              4              29 
[1] "CCDC135 MUTATION ANALYSIS"
[1] 3
  CCDC135 MUTATED CCDC135 WILD-TYPE 
                3                30 
  CCDC135 MUTATED CCDC135 WILD-TYPE 
                3                30 
[1] "CEP72 MUTATION ANALYSIS"
[1] 3
  CEP72 MUTATED CEP72 WILD-TYPE 
              3              30 
  CEP72 MUTATED CEP72 WILD-TYPE 
              3              30 
[1] "SMARCA2 MUTATION ANALYSIS"
[1] 3
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                3                30 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                3                30 
[1] "UBXN6 MUTATION ANALYSIS"
[1] 3
  UBXN6 MUTATED UBXN6 WILD-TYPE 
              3              30 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
              3              30 
[1] "YIPF2 MUTATION ANALYSIS"
[1] 3
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              3              30 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              3              30 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
             5             28 
  GNAS MUTATED GNAS WILD-TYPE 
             5             28 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               3               30 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               3               30 
[1] "PTPN21 MUTATION ANALYSIS"
[1] 3
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               3               30 
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               3               30 
[1] "TSC22D1 MUTATION ANALYSIS"
[1] 3
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                3                30 
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                3                30 
[1] "ZNF184 MUTATION ANALYSIS"
[1] 3
  ZNF184 MUTATED ZNF184 WILD-TYPE 
               4               29 
  ZNF184 MUTATED ZNF184 WILD-TYPE 
               4               29 
[1] "ANK3 MUTATION ANALYSIS"
[1] 3
  ANK3 MUTATED ANK3 WILD-TYPE 
             4             29 
  ANK3 MUTATED ANK3 WILD-TYPE 
             4             29 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "NUMBERPACKYEARSSMOKED"                 
[17] "YEAROFTOBACCOSMOKINGONSET"             
[18] "COMPLETENESS.OF.RESECTION"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 33 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FZ-5920 
         360          153          449            1          166           NA 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8637 
          NA           NA          396           28          361           NA 
TCGA-HZ-A49I TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          NA           11           13           NA          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS TCGA-IB-A5ST 
          17          329          300           NA           NA            8 
TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 TCGA-US-A779 
          NA          127          110          416          844           NA 
TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=3,	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:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS.OF.RESECTION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "NUMBERPACKYEARSSMOKED"    
 [9] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
[11] "RACE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 33 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=21, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T2 T3 T4 
 3 29  1 
[1] "table(vv)"
vv
T2+T3+T4 
      33 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T2 T3 T4 
 3 29  1 

$nClasses
[1] 1

$ClinVariableType
[1] "multiclass(1)"


T2+T3+T4 
      33 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=7, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=9, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = KRAS MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   11  4
  KRAS WILD-TYPE  7  1
  KRAS MUTATED KRAS WILD-TYPE 
            15              8 
  KRAS MUTATED KRAS WILD-TYPE 
             4              1 
$`KRAS MUTATED`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-HZ-A77O 
         153          449          166          396          361           11 
TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
          13         1989          476          851          329          300 
TCGA-IB-A5SS TCGA-IB-A6UG TCGA-OE-A75W 
        1991         1968          110 

$`KRAS WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A78T TCGA-HZ-7918 TCGA-IB-8126 TCGA-IB-A5ST TCGA-LB-A7SX 
         360            1           28           17            8          127 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  KRAS MUTATED KRAS WILD-TYPE 
            11              1 
  KRAS MUTATED KRAS WILD-TYPE 
          1991            844 
  KRAS MUTATED KRAS WILD-TYPE 
         361.0           77.5 
[1] "11.0 - 1991.0 (361.0)" "1.0 - 844.0 (77.5)"   
[1] "hr=" "3.3"
D1V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KRAS MUTATED          1         5        15         0        1
  KRAS WILD-TYPE        1         1         8         1        0
D1V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE IB             1              1
  STAGE IIA            5              1
  STAGE IIB           15              8
  STAGE III            0              1
  STAGE IV             1              0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  KRAS MUTATED         22
  KRAS WILD-TYPE       11
[1] "NOT AVAILABLE: table dimension [2x1]"
D1V5, binary
                cls
clus              0  1
  KRAS MUTATED    5 16
  KRAS WILD-TYPE  2  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      5   16
  KRAS WILD-TYPE    2    9
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            5              2
  1           16              9
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  KRAS MUTATED   13  1  8
  KRAS WILD-TYPE  6  0  5
D1V6, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  M0           13              6
  M1            1              0
  MX            8              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                cls
clus              0  1
  KRAS MUTATED    8 14
  KRAS WILD-TYPE  6  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      8   14
  KRAS WILD-TYPE    6    5
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            8              6
  MALE             14              5
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KRAS MUTATED                                    19
  KRAS WILD-TYPE                                   9
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KRAS MUTATED                                       2
  KRAS WILD-TYPE                                     1
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KRAS MUTATED                                                  1
  KRAS WILD-TYPE                                                1
D1V8, multiclass
                                                  clus
vv                                                 KRAS MUTATED KRAS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        19              9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2              1
  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"
D1V9, continuous
D1V10, binary
                cls
clus              0  1
  KRAS MUTATED   17  5
  KRAS WILD-TYPE  7  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     17    5
  KRAS WILD-TYPE    7    4
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           17              7
  R1            5              4
[1] 2 2
[1] FALSE
D1V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED       2                         1    19
  KRAS WILD-TYPE     0                         2     9
D1V12, multiclass
                           clus
vv                          KRAS MUTATED KRAS WILD-TYPE
  ASIAN                                2              0
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                               19              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   12  2
  TP53 WILD-TYPE  6  3
  TP53 MUTATED TP53 WILD-TYPE 
            14              9 
  TP53 MUTATED TP53 WILD-TYPE 
             2              3 
$`TP53 MUTATED`
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P 
         449            1          396          361           11           13 
TCGA-IB-7652 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         476          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W 
         127          110 

$`TP53 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A7DR TCGA-HZ-7918 TCGA-IB-7651 TCGA-IB-7885 
         360          153          166           28         1989          851 
TCGA-IB-8126 TCGA-Q3-A5QY TCGA-US-A776 
          17          416          844 

  TP53 MUTATED TP53 WILD-TYPE 
             1             17 
  TP53 MUTATED TP53 WILD-TYPE 
          1991           1989 
  TP53 MUTATED TP53 WILD-TYPE 
         314.5          360.0 
[1] "1.0 - 1991.0 (314.5)"  "17.0 - 1989.0 (360.0)"
[1] "hr=" "3.9"
D2V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TP53 MUTATED          1         3        14         0        0
  TP53 WILD-TYPE        1         3         9         1        1
D2V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE IB             1              1
  STAGE IIA            3              3
  STAGE IIB           14              9
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  TP53 MUTATED         18
  TP53 WILD-TYPE       15
[1] "NOT AVAILABLE: table dimension [2x1]"
D2V5, binary
                cls
clus              0  1
  TP53 MUTATED    4 14
  TP53 WILD-TYPE  3 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4   14
  TP53 WILD-TYPE    3   11
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            4              3
  1           14             11
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  TP53 MUTATED   10  0  8
  TP53 WILD-TYPE  9  1  5
D2V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           10              9
  M1            0              1
  MX            8              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                cls
clus              0  1
  TP53 MUTATED    8 10
  TP53 WILD-TYPE  6  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      8   10
  TP53 WILD-TYPE    6    9
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            8              6
  MALE             10              9
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TP53 MUTATED                                    16
  TP53 WILD-TYPE                                  12
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TP53 MUTATED                                       2
  TP53 WILD-TYPE                                     1
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TP53 MUTATED                                                  0
  TP53 WILD-TYPE                                                2
D2V8, multiclass
                                                  clus
vv                                                 TP53 MUTATED TP53 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        16             12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       2              1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA            0              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, continuous
D2V10, binary
                cls
clus              0  1
  TP53 MUTATED   13  5
  TP53 WILD-TYPE 11  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     13    5
  TP53 WILD-TYPE   11    4
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           13             11
  R1            5              4
[1] 2 2
[1] FALSE
D2V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       1                         2    15
  TP53 WILD-TYPE     1                         1    13
D2V12, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            2              1
  WHITE                               15             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = C19ORF55 MUTATION ANALYSIS
D3V1, survival
                    sevent
clus2                 0  1
  C19ORF55 MUTATED    3  1
  C19ORF55 WILD-TYPE 15  4
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                 4                 19 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                 1                  4 
$`C19ORF55 MUTATED`
TCGA-H8-A6C1 TCGA-HZ-A77P TCGA-IB-7651 TCGA-LB-A7SX 
         396           13         1989          127 

$`C19ORF55 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
         361           11          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W TCGA-Q3-A5QY 
         300         1991            8         1968          110          416 
TCGA-US-A776 
         844 

  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                13                  1 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
              1989               1991 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
             261.5              329.0 
[1] "13.0 - 1989.0 (261.5)" "1.0 - 1991.0 (329.0)" 
[1] "hr=" "1.2"
D3V2, continuous
                    vv
clus                 STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  C19ORF55 MUTATED          1         1         5         0        0
  C19ORF55 WILD-TYPE        1         5        18         1        1
D3V3, multiclass
           clus
vv          C19ORF55 MUTATED C19ORF55 WILD-TYPE
  STAGE IB                 1                  1
  STAGE IIA                1                  5
  STAGE IIB                5                 18
  STAGE III                0                  1
  STAGE IV                 0                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T2+T3+T4
  C19ORF55 MUTATED          7
  C19ORF55 WILD-TYPE       26
[1] "NOT AVAILABLE: table dimension [2x1]"
D3V5, binary
                    cls
clus                  0  1
  C19ORF55 MUTATED    2  5
  C19ORF55 WILD-TYPE  5 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      2    5
  C19ORF55 WILD-TYPE    5   20
   clus
vv  C19ORF55 MUTATED C19ORF55 WILD-TYPE
  0                2                  5
  1                5                 20
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  C19ORF55 MUTATED    3  0  4
  C19ORF55 WILD-TYPE 16  1  9
D3V6, multiclass
    clus
vv   C19ORF55 MUTATED C19ORF55 WILD-TYPE
  M0                3                 16
  M1                0                  1
  MX                4                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                    cls
clus                  0  1
  C19ORF55 MUTATED    4  3
  C19ORF55 WILD-TYPE 10 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      4    3
  C19ORF55 WILD-TYPE   10   16
        clus
vv       C19ORF55 MUTATED C19ORF55 WILD-TYPE
  FEMALE                4                 10
  MALE                  3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  C19ORF55 MUTATED                                     5
  C19ORF55 WILD-TYPE                                  23
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  C19ORF55 MUTATED                                       2
  C19ORF55 WILD-TYPE                                     1
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  C19ORF55 MUTATED                                                  0
  C19ORF55 WILD-TYPE                                                2
D3V8, multiclass
                                                  clus
vv                                                 C19ORF55 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 C19ORF55 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, continuous
D3V10, binary
                    cls
clus                  0  1
  C19ORF55 MUTATED    6  1
  C19ORF55 WILD-TYPE 18  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      6    1
  C19ORF55 WILD-TYPE   18    8
    clus
vv   C19ORF55 MUTATED C19ORF55 WILD-TYPE
  R0                6                 18
  R1                1                  8
[1] 2 2
[1] FALSE
D3V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C19ORF55 MUTATED       0                         2     5
  C19ORF55 WILD-TYPE     2                         1    23
D3V12, multiclass
                           clus
vv                          C19ORF55 MUTATED C19ORF55 WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                2                  1
  WHITE                                    5                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = B4GALT2 MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  B4GALT2 MUTATED    3  1
  B4GALT2 WILD-TYPE 15  4
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
                4                19 
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
                1                 4 
$`B4GALT2 MUTATED`
TCGA-F2-A44G TCGA-HZ-A77P TCGA-IB-7652 TCGA-US-A776 
         153           13          476          844 

$`B4GALT2 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
         361           11         1989          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY 
         416 

  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
               13                 1 
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
              844              1991 
  B4GALT2 MUTATED B4GALT2 WILD-TYPE 
            314.5             329.0 
[1] "13.0 - 844.0 (314.5)" "1.0 - 1991.0 (329.0)"
[1] "hr=" "4.2"
D4V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  B4GALT2 MUTATED          0         1         4         0        0
  B4GALT2 WILD-TYPE        2         5        19         1        1
D4V3, multiclass
           clus
vv          B4GALT2 MUTATED B4GALT2 WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               1                 5
  STAGE IIB               4                19
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  B4GALT2 MUTATED          5
  B4GALT2 WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D4V5, binary
                   cls
clus                 0  1
  B4GALT2 MUTATED    1  4
  B4GALT2 WILD-TYPE  6 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT2 MUTATED      1    4
  B4GALT2 WILD-TYPE    6   21
   clus
vv  B4GALT2 MUTATED B4GALT2 WILD-TYPE
  0               1                 6
  1               4                21
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  B4GALT2 MUTATED    2  0  3
  B4GALT2 WILD-TYPE 17  1 10
D4V6, multiclass
    clus
vv   B4GALT2 MUTATED B4GALT2 WILD-TYPE
  M0               2                17
  M1               0                 1
  MX               3                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                 0  1
  B4GALT2 MUTATED    3  2
  B4GALT2 WILD-TYPE 11 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT2 MUTATED      3    2
  B4GALT2 WILD-TYPE   11   17
        clus
vv       B4GALT2 MUTATED B4GALT2 WILD-TYPE
  FEMALE               3                11
  MALE                 2                17
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  B4GALT2 MUTATED                                     3
  B4GALT2 WILD-TYPE                                  25
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  B4GALT2 MUTATED                                       1
  B4GALT2 WILD-TYPE                                     2
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  B4GALT2 MUTATED                                                  1
  B4GALT2 WILD-TYPE                                                1
D4V8, multiclass
                                                  clus
vv                                                 B4GALT2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 B4GALT2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            2
  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"
D4V9, continuous
D4V10, binary
                   cls
clus                 0  1
  B4GALT2 MUTATED    3  2
  B4GALT2 WILD-TYPE 21  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT2 MUTATED      3    2
  B4GALT2 WILD-TYPE   21    7
    clus
vv   B4GALT2 MUTATED B4GALT2 WILD-TYPE
  R0               3                21
  R1               2                 7
[1] 2 2
[1] FALSE
D4V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  B4GALT2 MUTATED       1                         0     4
  B4GALT2 WILD-TYPE     1                         3    24
D4V12, multiclass
                           clus
vv                          B4GALT2 MUTATED B4GALT2 WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   4                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = CDKN2A MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED    2  2
  CDKN2A WILD-TYPE 16  3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               4               19 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               2                3 
$`CDKN2A MUTATED`
TCGA-HZ-A77O TCGA-IB-A5SS TCGA-IB-A6UG TCGA-OE-A75W 
          11         1991         1968          110 

$`CDKN2A WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          28          361           13         1989          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-LB-A7SX TCGA-Q3-A5QY 
          17          329          300            8          127          416 
TCGA-US-A776 
         844 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
              11                1 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1991             1989 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
            1039              329 
[1] "11.0 - 1991.0 (1039.0)" "1.0 - 1989.0 (329.0)"  
[1] "hr=" "2"  
D5V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CDKN2A MUTATED          0         1         5         0        0
  CDKN2A WILD-TYPE        2         5        18         1        1
D5V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              1                5
  STAGE IIB              5               18
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  CDKN2A MUTATED          6
  CDKN2A WILD-TYPE       27
[1] "NOT AVAILABLE: table dimension [2x1]"
D5V5, binary
                  cls
clus                0  1
  CDKN2A MUTATED    1  5
  CDKN2A WILD-TYPE  6 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1    5
  CDKN2A WILD-TYPE    6   20
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0              1                6
  1              5               20
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  CDKN2A MUTATED    4  0  2
  CDKN2A WILD-TYPE 15  1 11
D5V6, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  M0              4               15
  M1              0                1
  MX              2               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                  cls
clus                0  1
  CDKN2A MUTATED    2  4
  CDKN2A WILD-TYPE 12 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      2    4
  CDKN2A WILD-TYPE   12   15
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              2               12
  MALE                4               15
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDKN2A MUTATED                                     6
  CDKN2A WILD-TYPE                                  22
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDKN2A MUTATED                                       0
  CDKN2A WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDKN2A MUTATED                                                  0
  CDKN2A WILD-TYPE                                                2
D5V8, multiclass
                                                  clus
vv                                                 CDKN2A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 CDKN2A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, continuous
D5V10, binary
                  cls
clus                0  1
  CDKN2A MUTATED    5  1
  CDKN2A WILD-TYPE 19  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      5    1
  CDKN2A WILD-TYPE   19    8
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0              5               19
  R1              1                8
[1] 2 2
[1] FALSE
D5V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       0                         1     5
  CDKN2A WILD-TYPE     2                         2    23
D5V12, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                2
  WHITE                                  5               23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = NFIL3 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2              0  1
  NFIL3 MUTATED    3  1
  NFIL3 WILD-TYPE 15  4
  NFIL3 MUTATED NFIL3 WILD-TYPE 
              4              19 
  NFIL3 MUTATED NFIL3 WILD-TYPE 
              1               4 
$`NFIL3 MUTATED`
TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A5SO TCGA-OE-A75W 
          13         1989          329          110 

$`NFIL3 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28          361           11          476          851           17 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-Q3-A5QY 
         300         1991            8         1968          127          416 
TCGA-US-A776 
         844 

  NFIL3 MUTATED NFIL3 WILD-TYPE 
             13               1 
  NFIL3 MUTATED NFIL3 WILD-TYPE 
           1989            1991 
  NFIL3 MUTATED NFIL3 WILD-TYPE 
          219.5           360.0 
[1] "13.0 - 1989.0 (219.5)" "1.0 - 1991.0 (360.0)" 
[1] "hr=" "1.1"
D6V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NFIL3 MUTATED          0         1         5         0        0
  NFIL3 WILD-TYPE        2         5        18         1        1
D6V3, multiclass
           clus
vv          NFIL3 MUTATED NFIL3 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             5              18
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  NFIL3 MUTATED          6
  NFIL3 WILD-TYPE       27
[1] "NOT AVAILABLE: table dimension [2x1]"
D6V5, binary
                 cls
clus               0  1
  NFIL3 MUTATED    1  5
  NFIL3 WILD-TYPE  6 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFIL3 MUTATED      1    5
  NFIL3 WILD-TYPE    6   20
   clus
vv  NFIL3 MUTATED NFIL3 WILD-TYPE
  0             1               6
  1             5              20
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  NFIL3 MUTATED    3  0  3
  NFIL3 WILD-TYPE 16  1 10
D6V6, multiclass
    clus
vv   NFIL3 MUTATED NFIL3 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             3              10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                 cls
clus               0  1
  NFIL3 MUTATED    1  5
  NFIL3 WILD-TYPE 13 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFIL3 MUTATED      1    5
  NFIL3 WILD-TYPE   13   14
        clus
vv       NFIL3 MUTATED NFIL3 WILD-TYPE
  FEMALE             1              13
  MALE               5              14
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NFIL3 MUTATED                                     4
  NFIL3 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NFIL3 MUTATED                                       2
  NFIL3 WILD-TYPE                                     1
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NFIL3 MUTATED                                                  0
  NFIL3 WILD-TYPE                                                2
D6V8, multiclass
                                                  clus
vv                                                 NFIL3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NFIL3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, continuous
[1] "Remove cluster labels:" "NFIL3 MUTATED"         
clus
  NFIL3 MUTATED NFIL3 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"NFIL3 WILD-TYPE" "NFIL3 WILD-TYPE" "NFIL3 WILD-TYPE" "NFIL3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"NFIL3 WILD-TYPE" "NFIL3 WILD-TYPE" "NFIL3 WILD-TYPE" "NFIL3 WILD-TYPE" 
     TCGA-LB-A7SX 
"NFIL3 WILD-TYPE" 
D6V10, binary
                 cls
clus               0  1
  NFIL3 MUTATED    4  2
  NFIL3 WILD-TYPE 20  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFIL3 MUTATED      4    2
  NFIL3 WILD-TYPE   20    7
    clus
vv   NFIL3 MUTATED NFIL3 WILD-TYPE
  R0             4              20
  R1             2               7
[1] 2 2
[1] FALSE
D6V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFIL3 MUTATED       0                         0     6
  NFIL3 WILD-TYPE     2                         3    22
D6V12, multiclass
                           clus
vv                          NFIL3 MUTATED NFIL3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 6              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = OTOF MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  OTOF MUTATED    6  1
  OTOF WILD-TYPE 12  4
  OTOF MUTATED OTOF WILD-TYPE 
             7             16 
  OTOF MUTATED OTOF WILD-TYPE 
             1              4 
$`OTOF MUTATED`
TCGA-FB-A5VM TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A5ST 
         449           11           13         1989           17            8 
TCGA-US-A776 
         844 

$`OTOF WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153            1          166          396           28 
TCGA-HZ-7925 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
         361          476          851          329          300         1991 
TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY 
        1968          127          110          416 

  OTOF MUTATED OTOF WILD-TYPE 
             8              1 
  OTOF MUTATED OTOF WILD-TYPE 
          1989           1991 
  OTOF MUTATED OTOF WILD-TYPE 
          17.0          344.5 
[1] "8.0 - 1989.0 (17.0)"  "1.0 - 1991.0 (344.5)"
[1] "hr=" "1.5"
D7V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OTOF MUTATED          1         1         4         1        0
  OTOF WILD-TYPE        1         5        19         0        1
D7V3, multiclass
           clus
vv          OTOF MUTATED OTOF WILD-TYPE
  STAGE IB             1              1
  STAGE IIA            1              5
  STAGE IIB            4             19
  STAGE III            1              0
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  OTOF MUTATED          7
  OTOF WILD-TYPE       26
[1] "NOT AVAILABLE: table dimension [2x1]"
D7V5, binary
                cls
clus              0  1
  OTOF MUTATED    2  5
  OTOF WILD-TYPE  5 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTOF MUTATED      2    5
  OTOF WILD-TYPE    5   20
   clus
vv  OTOF MUTATED OTOF WILD-TYPE
  0            2              5
  1            5             20
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  OTOF MUTATED    4  0  3
  OTOF WILD-TYPE 15  1 10
D7V6, multiclass
    clus
vv   OTOF MUTATED OTOF WILD-TYPE
  M0            4             15
  M1            0              1
  MX            3             10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                cls
clus              0  1
  OTOF MUTATED    4  3
  OTOF WILD-TYPE 10 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTOF MUTATED      4    3
  OTOF WILD-TYPE   10   16
        clus
vv       OTOF MUTATED OTOF WILD-TYPE
  FEMALE            4             10
  MALE              3             16
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OTOF MUTATED                                     5
  OTOF WILD-TYPE                                  23
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OTOF MUTATED                                       1
  OTOF WILD-TYPE                                     2
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OTOF MUTATED                                                  1
  OTOF WILD-TYPE                                                1
D7V8, multiclass
                                                  clus
vv                                                 OTOF MUTATED OTOF WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5             23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1              2
  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"
D7V9, continuous
D7V10, binary
                cls
clus              0  1
  OTOF MUTATED    6  1
  OTOF WILD-TYPE 18  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTOF MUTATED      6    1
  OTOF WILD-TYPE   18    8
    clus
vv   OTOF MUTATED OTOF WILD-TYPE
  R0            6             18
  R1            1              8
[1] 2 2
[1] FALSE
D7V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTOF MUTATED       0                         0     7
  OTOF WILD-TYPE     2                         3    21
D7V12, multiclass
                           clus
vv                          OTOF MUTATED OTOF WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                7             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = IRS1 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2             0  1
  IRS1 MUTATED    2  1
  IRS1 WILD-TYPE 16  4
  IRS1 MUTATED IRS1 WILD-TYPE 
             3             20 
  IRS1 MUTATED IRS1 WILD-TYPE 
             1              4 
$`IRS1 MUTATED`
TCGA-F2-7273 TCGA-HZ-A77O TCGA-IB-A5SP 
         360           11          300 

$`IRS1 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           13         1989          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         329         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  IRS1 MUTATED IRS1 WILD-TYPE 
            11              1 
  IRS1 MUTATED IRS1 WILD-TYPE 
           360           1991 
  IRS1 MUTATED IRS1 WILD-TYPE 
           300            345 
[1] "11.0 - 360.0 (300.0)" "1.0 - 1991.0 (345.0)"
[1] "hr=" "8.1"
D8V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  IRS1 MUTATED          0         1         5         0        0
  IRS1 WILD-TYPE        2         5        18         1        1
D8V3, multiclass
           clus
vv          IRS1 MUTATED IRS1 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            1              5
  STAGE IIB            5             18
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  IRS1 MUTATED          6
  IRS1 WILD-TYPE       27
[1] "NOT AVAILABLE: table dimension [2x1]"
D8V5, binary
                cls
clus              0  1
  IRS1 MUTATED    1  5
  IRS1 WILD-TYPE  6 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      1    5
  IRS1 WILD-TYPE    6   20
   clus
vv  IRS1 MUTATED IRS1 WILD-TYPE
  0            1              6
  1            5             20
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  IRS1 MUTATED    2  0  4
  IRS1 WILD-TYPE 17  1  9
D8V6, multiclass
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  M0            2             17
  M1            0              1
  MX            4              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                cls
clus              0  1
  IRS1 MUTATED    2  4
  IRS1 WILD-TYPE 12 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      2    4
  IRS1 WILD-TYPE   12   15
        clus
vv       IRS1 MUTATED IRS1 WILD-TYPE
  FEMALE            2             12
  MALE              4             15
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IRS1 MUTATED                                     5
  IRS1 WILD-TYPE                                  23
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IRS1 MUTATED                                       1
  IRS1 WILD-TYPE                                     2
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IRS1 MUTATED                                                  0
  IRS1 WILD-TYPE                                                2
D8V8, multiclass
                                                  clus
vv                                                 IRS1 MUTATED IRS1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5             23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1              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"
D8V9, continuous
D8V10, binary
                cls
clus              0  1
  IRS1 MUTATED    3  3
  IRS1 WILD-TYPE 21  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS1 MUTATED      3    3
  IRS1 WILD-TYPE   21    6
    clus
vv   IRS1 MUTATED IRS1 WILD-TYPE
  R0            3             21
  R1            3              6
[1] 2 2
[1] FALSE
D8V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRS1 MUTATED       0                         1     5
  IRS1 WILD-TYPE     2                         2    23
D8V12, multiclass
                           clus
vv                          IRS1 MUTATED IRS1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                5             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = GAS2L2 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2               0  1
  GAS2L2 MUTATED    3  1
  GAS2L2 WILD-TYPE 15  4
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               4               19 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
               1                4 
$`GAS2L2 MUTATED`
TCGA-FB-A7DR TCGA-IB-7651 TCGA-IB-8126 TCGA-LB-A7SX 
         166         1989           17          127 

$`GAS2L2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449            1          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
         361           11           13          476          851          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W TCGA-Q3-A5QY 
         300         1991            8         1968          110          416 
TCGA-US-A776 
         844 

  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
              17                1 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
            1989             1991 
  GAS2L2 MUTATED GAS2L2 WILD-TYPE 
           146.5            360.0 
[1] "17.0 - 1989.0 (146.5)" "1.0 - 1991.0 (360.0)" 
[1] "hr=" "1.1"
D9V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GAS2L2 MUTATED          0         1         3         1        0
  GAS2L2 WILD-TYPE        2         5        20         0        1
D9V3, multiclass
           clus
vv          GAS2L2 MUTATED GAS2L2 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              1                5
  STAGE IIB              3               20
  STAGE III              1                0
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  GAS2L2 MUTATED          5
  GAS2L2 WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D9V5, binary
                  cls
clus                0  1
  GAS2L2 MUTATED    0  4
  GAS2L2 WILD-TYPE  7 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED      0    4
  GAS2L2 WILD-TYPE    7   21
   clus
vv  GAS2L2 MUTATED GAS2L2 WILD-TYPE
  0              0                7
  1              4               21
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  GAS2L2 MUTATED    4  0  1
  GAS2L2 WILD-TYPE 15  1 12
D9V6, multiclass
    clus
vv   GAS2L2 MUTATED GAS2L2 WILD-TYPE
  M0              4               15
  M1              0                1
  MX              1               12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                  cls
clus                0  1
  GAS2L2 MUTATED    3  2
  GAS2L2 WILD-TYPE 11 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED      3    2
  GAS2L2 WILD-TYPE   11   17
        clus
vv       GAS2L2 MUTATED GAS2L2 WILD-TYPE
  FEMALE              3               11
  MALE                2               17
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GAS2L2 MUTATED                                     4
  GAS2L2 WILD-TYPE                                  24
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GAS2L2 MUTATED                                       0
  GAS2L2 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GAS2L2 MUTATED                                                  1
  GAS2L2 WILD-TYPE                                                1
D9V8, multiclass
                                                  clus
vv                                                 GAS2L2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
                                                  clus
vv                                                 GAS2L2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  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"
D9V9, continuous
D9V10, binary
                  cls
clus                0  1
  GAS2L2 MUTATED    3  2
  GAS2L2 WILD-TYPE 21  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAS2L2 MUTATED      3    2
  GAS2L2 WILD-TYPE   21    7
    clus
vv   GAS2L2 MUTATED GAS2L2 WILD-TYPE
  R0              3               21
  R1              2                7
[1] 2 2
[1] FALSE
D9V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GAS2L2 MUTATED       1                         2     2
  GAS2L2 WILD-TYPE     1                         1    26
D9V12, multiclass
                           clus
vv                          GAS2L2 MUTATED GAS2L2 WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              2                1
  WHITE                                  2               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = RBM10 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  RBM10 MUTATED    3  1
  RBM10 WILD-TYPE 15  4
  RBM10 MUTATED RBM10 WILD-TYPE 
              4              19 
  RBM10 MUTATED RBM10 WILD-TYPE 
              1               4 
$`RBM10 MUTATED`
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-8126 TCGA-US-A776 
        1989          476           17          844 

$`RBM10 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7885 TCGA-IB-A5SO 
          28          361           11           13          851          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY 
         416 

  RBM10 MUTATED RBM10 WILD-TYPE 
             17               1 
  RBM10 MUTATED RBM10 WILD-TYPE 
           1989            1991 
  RBM10 MUTATED RBM10 WILD-TYPE 
            660             300 
[1] "17.0 - 1989.0 (660.0)" "1.0 - 1991.0 (300.0)" 
[1] "hr=" "1.5"
D10V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RBM10 MUTATED          0         1         3         1        0
  RBM10 WILD-TYPE        2         5        20         0        1
D10V3, multiclass
           clus
vv          RBM10 MUTATED RBM10 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             3              20
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  RBM10 MUTATED          5
  RBM10 WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D10V5, binary
                 cls
clus               0  1
  RBM10 MUTATED    1  4
  RBM10 WILD-TYPE  6 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      1    4
  RBM10 WILD-TYPE    6   21
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             1               6
  1             4              21
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  RBM10 MUTATED    3  0  2
  RBM10 WILD-TYPE 16  1 11
D10V6, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                 cls
clus               0  1
  RBM10 MUTATED    3  2
  RBM10 WILD-TYPE 11 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      3    2
  RBM10 WILD-TYPE   11   17
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             3              11
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM10 MUTATED                                     4
  RBM10 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM10 MUTATED                                       0
  RBM10 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM10 MUTATED                                                  1
  RBM10 WILD-TYPE                                                1
D10V8, multiclass
                                                  clus
vv                                                 RBM10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 RBM10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  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"
D10V9, continuous
[1] "Remove cluster labels:" "RBM10 MUTATED"         
clus
  RBM10 MUTATED RBM10 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" "RBM10 WILD-TYPE" 
     TCGA-OE-A75W 
"RBM10 WILD-TYPE" 
D10V10, binary
                 cls
clus               0  1
  RBM10 MUTATED    3  2
  RBM10 WILD-TYPE 21  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      3    2
  RBM10 WILD-TYPE   21    7
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0             3              21
  R1             2               7
[1] 2 2
[1] FALSE
D10V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED       1                         0     4
  RBM10 WILD-TYPE     1                         3    24
D10V12, multiclass
                           clus
vv                          RBM10 MUTATED RBM10 WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = APP MUTATION ANALYSIS
D11V1, survival
               sevent
clus2            0  1
  APP MUTATED    3  1
  APP WILD-TYPE 15  4
  APP MUTATED APP WILD-TYPE 
            4            19 
  APP MUTATED APP WILD-TYPE 
            1             4 
$`APP MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7885 TCGA-LB-A7SX 
         361         1989          851          127 

$`APP WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO 
          28           11           13          476           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W TCGA-Q3-A5QY 
         300         1991            8         1968          110          416 
TCGA-US-A776 
         844 

  APP MUTATED APP WILD-TYPE 
          127             1 
  APP MUTATED APP WILD-TYPE 
         1989          1991 
  APP MUTATED APP WILD-TYPE 
          606           300 
[1] "127.0 - 1989.0 (606.0)" "1.0 - 1991.0 (300.0)"  
[1] "hr=" "1.5"
D11V2, continuous
               vv
clus            STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  APP MUTATED          0         1         5         0        0
  APP WILD-TYPE        2         5        18         1        1
D11V3, multiclass
           clus
vv          APP MUTATED APP WILD-TYPE
  STAGE IB            0             2
  STAGE IIA           1             5
  STAGE IIB           5            18
  STAGE III           0             1
  STAGE IV            0             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T2+T3+T4
  APP MUTATED          6
  APP WILD-TYPE       27
[1] "NOT AVAILABLE: table dimension [2x1]"
D11V5, binary
               cls
clus             0  1
  APP MUTATED    1  5
  APP WILD-TYPE  6 20
[1] "tbl2"
               cls
clus            [,1] [,2]
  APP MUTATED      1    5
  APP WILD-TYPE    6   20
   clus
vv  APP MUTATED APP WILD-TYPE
  0           1             6
  1           5            20
[1] 2 2
[1] FALSE
               vv
clus            M0 M1 MX
  APP MUTATED    3  0  3
  APP WILD-TYPE 16  1 10
D11V6, multiclass
    clus
vv   APP MUTATED APP WILD-TYPE
  M0           3            16
  M1           0             1
  MX           3            10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
               cls
clus             0  1
  APP MUTATED    4  2
  APP WILD-TYPE 10 17
[1] "tbl2"
               cls
clus            [,1] [,2]
  APP MUTATED      4    2
  APP WILD-TYPE   10   17
        clus
vv       APP MUTATED APP WILD-TYPE
  FEMALE           4            10
  MALE             2            17
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  APP MUTATED                                     6
  APP WILD-TYPE                                  22
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  APP MUTATED                                       0
  APP WILD-TYPE                                     3
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  APP MUTATED                                                  0
  APP WILD-TYPE                                                2
D11V8, multiclass
                                                  clus
vv                                                 APP MUTATED APP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        6            22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0             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"
D11V9, continuous
D11V10, binary
               cls
clus             0  1
  APP MUTATED    5  1
  APP WILD-TYPE 19  8
[1] "tbl2"
               cls
clus            [,1] [,2]
  APP MUTATED      5    1
  APP WILD-TYPE   19    8
    clus
vv   APP MUTATED APP WILD-TYPE
  R0           5            19
  R1           1             8
[1] 2 2
[1] FALSE
D11V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APP MUTATED       0                         1     5
  APP WILD-TYPE     2                         2    23
D11V12, multiclass
                           clus
vv                          APP MUTATED APP WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           1             2
  WHITE                               5            23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = IPP MUTATION ANALYSIS
D12V1, survival
               sevent
clus2            0  1
  IPP MUTATED    2  1
  IPP WILD-TYPE 16  4
  IPP MUTATED IPP WILD-TYPE 
            3            20 
  IPP MUTATED IPP WILD-TYPE 
            1             4 
$`IPP MUTATED`
TCGA-FB-A5VM TCGA-IB-7651 TCGA-Q3-A5QY 
         449         1989          416 

$`IPP WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-US-A776 
         110          844 

  IPP MUTATED IPP WILD-TYPE 
          416             1 
  IPP MUTATED IPP WILD-TYPE 
         1989          1991 
  IPP MUTATED IPP WILD-TYPE 
          449           233 
[1] "416.0 - 1989.0 (449.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D12V2, continuous
               vv
clus            STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  IPP MUTATED          2         0         2         0        0
  IPP WILD-TYPE        0         6        21         1        1
D12V3, multiclass
           clus
vv          IPP MUTATED IPP WILD-TYPE
  STAGE IB            2             0
  STAGE IIA           0             6
  STAGE IIB           2            21
  STAGE III           0             1
  STAGE IV            0             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T2+T3+T4
  IPP MUTATED          4
  IPP WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D12V5, binary
               cls
clus             0  1
  IPP MUTATED    2  2
  IPP WILD-TYPE  5 23
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      2    2
  IPP WILD-TYPE    5   23
   clus
vv  IPP MUTATED IPP WILD-TYPE
  0           2             5
  1           2            23
[1] 2 2
[1] FALSE
               vv
clus            M0 M1 MX
  IPP MUTATED    3  0  1
  IPP WILD-TYPE 16  1 12
D12V6, multiclass
    clus
vv   IPP MUTATED IPP WILD-TYPE
  M0           3            16
  M1           0             1
  MX           1            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
               cls
clus             0  1
  IPP MUTATED    2  2
  IPP WILD-TYPE 12 17
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      2    2
  IPP WILD-TYPE   12   17
        clus
vv       IPP MUTATED IPP WILD-TYPE
  FEMALE           2            12
  MALE             2            17
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IPP MUTATED                                     4
  IPP WILD-TYPE                                  24
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IPP MUTATED                                       0
  IPP WILD-TYPE                                     3
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IPP MUTATED                                                  0
  IPP WILD-TYPE                                                2
D12V8, multiclass
                                                  clus
vv                                                 IPP MUTATED IPP WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4            24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0             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"
D12V9, continuous
[1] "Remove cluster labels:" "IPP MUTATED"           
clus
  IPP MUTATED IPP WILD-TYPE 
            2             9 
   TCGA-FB-A78T    TCGA-FB-A7DR    TCGA-H8-A6C1    TCGA-IB-7885    TCGA-IB-8126 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
   TCGA-IB-A5SS    TCGA-IB-A6UG    TCGA-LB-A7SX    TCGA-OE-A75W 
"IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" "IPP WILD-TYPE" 
D12V10, binary
               cls
clus             0  1
  IPP MUTATED    4  0
  IPP WILD-TYPE 20  9
[1] "tbl2"
               cls
clus            [,1] [,2]
  IPP MUTATED      4    0
  IPP WILD-TYPE   20    9
    clus
vv   IPP MUTATED IPP WILD-TYPE
  R0           4            20
  R1           0             9
[1] 2 2
[1] FALSE
D12V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IPP MUTATED       0                         0     4
  IPP WILD-TYPE     2                         3    24
D12V12, multiclass
                           clus
vv                          IPP MUTATED IPP WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0             3
  WHITE                               4            24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = MAMLD1 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2               0  1
  MAMLD1 MUTATED    5  2
  MAMLD1 WILD-TYPE 13  3
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               7               16 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
               2                3 
$`MAMLD1 MUTATED`
TCGA-F2-7273 TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-IB-7651 TCGA-IB-A5SP TCGA-OE-A75W 
         360          166          396         1989          300          110 
TCGA-Q3-A5QY 
         416 

$`MAMLD1 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O 
         153          449            1           28          361           11 
TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS 
          13          476          851           17          329         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-US-A776 
           8         1968          127          844 

  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
             110                1 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
            1989             1991 
  MAMLD1 MUTATED MAMLD1 WILD-TYPE 
             360              241 
[1] "110.0 - 1989.0 (360.0)" "1.0 - 1991.0 (241.0)"  
[1] "hr=" "1.5"
D13V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MAMLD1 MUTATED          0         4         3         0        0
  MAMLD1 WILD-TYPE        2         2        20         1        1
D13V3, multiclass
           clus
vv          MAMLD1 MUTATED MAMLD1 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              4                2
  STAGE IIB              3               20
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  MAMLD1 MUTATED          7
  MAMLD1 WILD-TYPE       26
[1] "NOT AVAILABLE: table dimension [2x1]"
D13V5, binary
                  cls
clus                0  1
  MAMLD1 MUTATED    3  3
  MAMLD1 WILD-TYPE  4 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMLD1 MUTATED      3    3
  MAMLD1 WILD-TYPE    4   22
   clus
vv  MAMLD1 MUTATED MAMLD1 WILD-TYPE
  0              3                4
  1              3               22
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  MAMLD1 MUTATED    5  0  2
  MAMLD1 WILD-TYPE 14  1 11
D13V6, multiclass
    clus
vv   MAMLD1 MUTATED MAMLD1 WILD-TYPE
  M0              5               14
  M1              0                1
  MX              2               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                  cls
clus                0  1
  MAMLD1 MUTATED    1  6
  MAMLD1 WILD-TYPE 13 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMLD1 MUTATED      1    6
  MAMLD1 WILD-TYPE   13   13
        clus
vv       MAMLD1 MUTATED MAMLD1 WILD-TYPE
  FEMALE              1               13
  MALE                6               13
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAMLD1 MUTATED                                     5
  MAMLD1 WILD-TYPE                                  23
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAMLD1 MUTATED                                       1
  MAMLD1 WILD-TYPE                                     2
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAMLD1 MUTATED                                                  1
  MAMLD1 WILD-TYPE                                                1
D13V8, multiclass
                                                  clus
vv                                                 MAMLD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
                                                  clus
vv                                                 MAMLD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  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"
D13V9, continuous
D13V10, binary
                  cls
clus                0  1
  MAMLD1 MUTATED    5  2
  MAMLD1 WILD-TYPE 19  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAMLD1 MUTATED      5    2
  MAMLD1 WILD-TYPE   19    7
    clus
vv   MAMLD1 MUTATED MAMLD1 WILD-TYPE
  R0              5               19
  R1              2                7
[1] 2 2
[1] FALSE
D13V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAMLD1 MUTATED       1                         1     5
  MAMLD1 WILD-TYPE     1                         2    23
D13V12, multiclass
                           clus
vv                          MAMLD1 MUTATED MAMLD1 WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              1                2
  WHITE                                  5               23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = ARHGAP18 MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                 0  1
  ARHGAP18 MUTATED    2  1
  ARHGAP18 WILD-TYPE 16  4
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 3                 20 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 1                  4 
$`ARHGAP18 MUTATED`
TCGA-F2-7273 TCGA-H8-A6C1 TCGA-IB-8126 
         360          396           17 

$`ARHGAP18 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 TCGA-HZ-7925 
         153          449            1          166           28          361 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
          11           13         1989          476          851          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                17                  1 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
               396               1991 
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
             360.0              314.5 
[1] "17.0 - 396.0 (360.0)" "1.0 - 1991.0 (314.5)"
[1] "hr=" "5.4"
D14V2, continuous
                    vv
clus                 STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ARHGAP18 MUTATED          0         1         1         1        0
  ARHGAP18 WILD-TYPE        2         5        22         0        1
D14V3, multiclass
           clus
vv          ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  STAGE IB                 0                  2
  STAGE IIA                1                  5
  STAGE IIB                1                 22
  STAGE III                1                  0
  STAGE IV                 0                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T2+T3+T4
  ARHGAP18 MUTATED          3
  ARHGAP18 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D14V5, binary
                    cls
clus                  0  1
  ARHGAP18 MUTATED    1  2
  ARHGAP18 WILD-TYPE  6 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      1    2
  ARHGAP18 WILD-TYPE    6   23
   clus
vv  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  0                1                  6
  1                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  ARHGAP18 MUTATED    2  0  1
  ARHGAP18 WILD-TYPE 17  1 12
D14V6, multiclass
    clus
vv   ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  M0                2                 17
  M1                0                  1
  MX                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                    cls
clus                  0  1
  ARHGAP18 MUTATED    1  2
  ARHGAP18 WILD-TYPE 13 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      1    2
  ARHGAP18 WILD-TYPE   13   17
        clus
vv       ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  FEMALE                1                 13
  MALE                  2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARHGAP18 MUTATED                                     2
  ARHGAP18 WILD-TYPE                                  26
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARHGAP18 MUTATED                                       1
  ARHGAP18 WILD-TYPE                                     2
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARHGAP18 MUTATED                                                  0
  ARHGAP18 WILD-TYPE                                                2
D14V8, multiclass
                                                  clus
vv                                                 ARHGAP18 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 ARHGAP18 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, continuous
[1] "Remove cluster labels:" "ARHGAP18 MUTATED"      
clus
  ARHGAP18 MUTATED ARHGAP18 WILD-TYPE 
                 2                  9 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-A7DR 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-IB-7651         TCGA-IB-7885         TCGA-IB-A5SS 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-LB-A7SX         TCGA-OE-A75W 
"ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" "ARHGAP18 WILD-TYPE" 
D14V10, binary
                    cls
clus                  0  1
  ARHGAP18 MUTATED    1  2
  ARHGAP18 WILD-TYPE 23  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP18 MUTATED      1    2
  ARHGAP18 WILD-TYPE   23    7
    clus
vv   ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  R0                1                 23
  R1                2                  7
[1] 2 2
[1] FALSE
D14V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP18 MUTATED       0                         1     2
  ARHGAP18 WILD-TYPE     2                         2    26
D14V12, multiclass
                           clus
vv                          ARHGAP18 MUTATED ARHGAP18 WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                    2                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = PHF8 MUTATION ANALYSIS
D15V1, survival
                sevent
clus2             0  1
  PHF8 MUTATED    3  0
  PHF8 WILD-TYPE 15  5
  PHF8 MUTATED PHF8 WILD-TYPE 
             3             20 
  PHF8 MUTATED PHF8 WILD-TYPE 
             0              5 
$`PHF8 MUTATED`
TCGA-LB-A7SX TCGA-OE-A75W TCGA-US-A776 
         127          110          844 

$`PHF8 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 
          28          361           11           13         1989          476 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
         851           17          329          300         1991            8 
TCGA-IB-A6UG TCGA-Q3-A5QY 
        1968          416 

  PHF8 MUTATED PHF8 WILD-TYPE 
           110              1 
  PHF8 MUTATED PHF8 WILD-TYPE 
           844           1991 
  PHF8 MUTATED PHF8 WILD-TYPE 
         127.0          344.5 
[1] "110.0 - 844.0 (127.0)" "1.0 - 1991.0 (344.5)" 
[1] "hr="     "7.5e+07"
D15V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PHF8 MUTATED          0         3         1         0        0
  PHF8 WILD-TYPE        2         3        22         1        1
D15V3, multiclass
           clus
vv          PHF8 MUTATED PHF8 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            3              3
  STAGE IIB            1             22
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  PHF8 MUTATED          4
  PHF8 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D15V5, binary
                cls
clus              0  1
  PHF8 MUTATED    3  1
  PHF8 WILD-TYPE  4 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF8 MUTATED      3    1
  PHF8 WILD-TYPE    4   24
   clus
vv  PHF8 MUTATED PHF8 WILD-TYPE
  0            3              4
  1            1             24
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  PHF8 MUTATED    2  0  2
  PHF8 WILD-TYPE 17  1 11
D15V6, multiclass
    clus
vv   PHF8 MUTATED PHF8 WILD-TYPE
  M0            2             17
  M1            0              1
  MX            2             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                cls
clus              0  1
  PHF8 MUTATED    1  3
  PHF8 WILD-TYPE 13 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF8 MUTATED      1    3
  PHF8 WILD-TYPE   13   16
        clus
vv       PHF8 MUTATED PHF8 WILD-TYPE
  FEMALE            1             13
  MALE              3             16
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PHF8 MUTATED                                     3
  PHF8 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PHF8 MUTATED                                       0
  PHF8 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PHF8 MUTATED                                                  1
  PHF8 WILD-TYPE                                                1
D15V8, multiclass
                                                  clus
vv                                                 PHF8 MUTATED PHF8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              3
  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"
D15V9, continuous
[1] "Remove cluster labels:" "PHF8 MUTATED"          
clus
  PHF8 MUTATED PHF8 WILD-TYPE 
             2              9 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"PHF8 WILD-TYPE" "PHF8 WILD-TYPE" "PHF8 WILD-TYPE" "PHF8 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS 
"PHF8 WILD-TYPE" "PHF8 WILD-TYPE" "PHF8 WILD-TYPE" "PHF8 WILD-TYPE" 
    TCGA-IB-A6UG 
"PHF8 WILD-TYPE" 
D15V10, binary
                cls
clus              0  1
  PHF8 MUTATED    3  1
  PHF8 WILD-TYPE 21  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF8 MUTATED      3    1
  PHF8 WILD-TYPE   21    8
    clus
vv   PHF8 MUTATED PHF8 WILD-TYPE
  R0            3             21
  R1            1              8
[1] 2 2
[1] FALSE
D15V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PHF8 MUTATED       0                         1     3
  PHF8 WILD-TYPE     2                         2    25
D15V12, multiclass
                           clus
vv                          PHF8 MUTATED PHF8 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = THBS4 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2              0  1
  THBS4 MUTATED    4  1
  THBS4 WILD-TYPE 14  4
  THBS4 MUTATED THBS4 WILD-TYPE 
              5              18 
  THBS4 MUTATED THBS4 WILD-TYPE 
              1               4 
$`THBS4 MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-8126 TCGA-OE-A75W TCGA-US-A776 
        1989          851           17          110          844 

$`THBS4 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-A5SO 
          28          361           11           13          476          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-Q3-A5QY 
         300         1991            8         1968          127          416 

  THBS4 MUTATED THBS4 WILD-TYPE 
             17               1 
  THBS4 MUTATED THBS4 WILD-TYPE 
           1989            1991 
  THBS4 MUTATED THBS4 WILD-TYPE 
          844.0           314.5 
[1] "17.0 - 1989.0 (844.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.5"
D16V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  THBS4 MUTATED          1         2         2         1        0
  THBS4 WILD-TYPE        1         4        21         0        1
D16V3, multiclass
           clus
vv          THBS4 MUTATED THBS4 WILD-TYPE
  STAGE IB              1               1
  STAGE IIA             2               4
  STAGE IIB             2              21
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  THBS4 MUTATED          6
  THBS4 WILD-TYPE       27
[1] "NOT AVAILABLE: table dimension [2x1]"
D16V5, binary
                 cls
clus               0  1
  THBS4 MUTATED    3  3
  THBS4 WILD-TYPE  4 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS4 MUTATED      3    3
  THBS4 WILD-TYPE    4   22
   clus
vv  THBS4 MUTATED THBS4 WILD-TYPE
  0             3               4
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  THBS4 MUTATED    5  0  1
  THBS4 WILD-TYPE 14  1 12
D16V6, multiclass
    clus
vv   THBS4 MUTATED THBS4 WILD-TYPE
  M0             5              14
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                 cls
clus               0  1
  THBS4 MUTATED    4  2
  THBS4 WILD-TYPE 10 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS4 MUTATED      4    2
  THBS4 WILD-TYPE   10   17
        clus
vv       THBS4 MUTATED THBS4 WILD-TYPE
  FEMALE             4              10
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  THBS4 MUTATED                                     5
  THBS4 WILD-TYPE                                  23
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  THBS4 MUTATED                                       0
  THBS4 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  THBS4 MUTATED                                                  1
  THBS4 WILD-TYPE                                                1
D16V8, multiclass
                                                  clus
vv                                                 THBS4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 THBS4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  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"
D16V9, continuous
D16V10, binary
                 cls
clus               0  1
  THBS4 MUTATED    5  1
  THBS4 WILD-TYPE 19  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS4 MUTATED      5    1
  THBS4 WILD-TYPE   19    8
    clus
vv   THBS4 MUTATED THBS4 WILD-TYPE
  R0             5              19
  R1             1               8
[1] 2 2
[1] FALSE
D16V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  THBS4 MUTATED       0                         0     6
  THBS4 WILD-TYPE     2                         3    22
D16V12, multiclass
                           clus
vv                          THBS4 MUTATED THBS4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 6              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = SMAD4 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2              0  1
  SMAD4 MUTATED    3  2
  SMAD4 WILD-TYPE 15  3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              5              18 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              2               3 
$`SMAD4 MUTATED`
TCGA-FB-A78T TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-A5SP TCGA-IB-A5SS 
           1          361         1989          300         1991 

$`SMAD4 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
          11           13          476          851           17          329 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
           8         1968          127          110          416          844 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
              1               8 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
           1991            1968 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          361.0           247.5 
[1] "1.0 - 1991.0 (361.0)" "8.0 - 1968.0 (247.5)"
[1] "hr="     "1.7e+09"
D17V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SMAD4 MUTATED          0         1         5         0        1
  SMAD4 WILD-TYPE        2         5        18         1        0
D17V3, multiclass
           clus
vv          SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             5              18
  STAGE III             0               1
  STAGE IV              1               0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  SMAD4 MUTATED          7
  SMAD4 WILD-TYPE       26
[1] "NOT AVAILABLE: table dimension [2x1]"
D17V5, binary
                 cls
clus               0  1
  SMAD4 MUTATED    1  6
  SMAD4 WILD-TYPE  6 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      1    6
  SMAD4 WILD-TYPE    6   19
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0             1               6
  1             6              19
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  SMAD4 MUTATED    4  1  2
  SMAD4 WILD-TYPE 15  0 11
D17V6, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  M0             4              15
  M1             1               0
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                 cls
clus               0  1
  SMAD4 MUTATED    3  4
  SMAD4 WILD-TYPE 11 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      3    4
  SMAD4 WILD-TYPE   11   15
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE             3              11
  MALE               4              15
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMAD4 MUTATED                                     7
  SMAD4 WILD-TYPE                                  21
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMAD4 MUTATED                                       0
  SMAD4 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMAD4 MUTATED                                                  0
  SMAD4 WILD-TYPE                                                2
D17V8, multiclass
                                                  clus
vv                                                 SMAD4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SMAD4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, continuous
D17V10, binary
                 cls
clus               0  1
  SMAD4 MUTATED    6  1
  SMAD4 WILD-TYPE 18  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      6    1
  SMAD4 WILD-TYPE   18    8
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0             6              18
  R1             1               8
[1] 2 2
[1] FALSE
D17V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED       0                         0     7
  SMAD4 WILD-TYPE     2                         3    21
D17V12, multiclass
                           clus
vv                          SMAD4 MUTATED SMAD4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 7              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = PTPRF MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2              0  1
  PTPRF MUTATED    2  3
  PTPRF WILD-TYPE 16  2
  PTPRF MUTATED PTPRF WILD-TYPE 
              5              18 
  PTPRF MUTATED PTPRF WILD-TYPE 
              3               2 
$`PTPRF MUTATED`
TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A5SS TCGA-IB-A6UG TCGA-LB-A7SX 
        1989           17         1991         1968          127 

$`PTPRF WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         329          300            8          110          416          844 

  PTPRF MUTATED PTPRF WILD-TYPE 
             17               1 
  PTPRF MUTATED PTPRF WILD-TYPE 
           1991             851 
  PTPRF MUTATED PTPRF WILD-TYPE 
         1968.0           314.5 
[1] "17.0 - 1991.0 (1968.0)" "1.0 - 851.0 (314.5)"   
[1] "hr="     "2.8e+08"
D18V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PTPRF MUTATED          0         0         5         1        0
  PTPRF WILD-TYPE        2         6        18         0        1
D18V3, multiclass
           clus
vv          PTPRF MUTATED PTPRF WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             5              18
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  PTPRF MUTATED          6
  PTPRF WILD-TYPE       27
[1] "NOT AVAILABLE: table dimension [2x1]"
D18V5, binary
                 cls
clus               0  1
  PTPRF MUTATED    0  6
  PTPRF WILD-TYPE  7 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRF MUTATED      0    6
  PTPRF WILD-TYPE    7   19
   clus
vv  PTPRF MUTATED PTPRF WILD-TYPE
  0             0               7
  1             6              19
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  PTPRF MUTATED    4  0  2
  PTPRF WILD-TYPE 15  1 11
D18V6, multiclass
    clus
vv   PTPRF MUTATED PTPRF WILD-TYPE
  M0             4              15
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                 cls
clus               0  1
  PTPRF MUTATED    5  1
  PTPRF WILD-TYPE  9 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRF MUTATED      5    1
  PTPRF WILD-TYPE    9   18
        clus
vv       PTPRF MUTATED PTPRF WILD-TYPE
  FEMALE             5               9
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PTPRF MUTATED                                     6
  PTPRF WILD-TYPE                                  22
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PTPRF MUTATED                                       0
  PTPRF WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PTPRF MUTATED                                                  0
  PTPRF WILD-TYPE                                                2
D18V8, multiclass
                                                  clus
vv                                                 PTPRF MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PTPRF WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, continuous
D18V10, binary
                 cls
clus               0  1
  PTPRF MUTATED    3  3
  PTPRF WILD-TYPE 21  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRF MUTATED      3    3
  PTPRF WILD-TYPE   21    6
    clus
vv   PTPRF MUTATED PTPRF WILD-TYPE
  R0             3              21
  R1             3               6
[1] 2 2
[1] FALSE
D18V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPRF MUTATED       0                         1     5
  PTPRF WILD-TYPE     2                         2    23
D18V12, multiclass
                           clus
vv                          PTPRF MUTATED PTPRF WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 5              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = MED12 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2              0  1
  MED12 MUTATED    2  2
  MED12 WILD-TYPE 16  3
  MED12 MUTATED MED12 WILD-TYPE 
              4              19 
  MED12 MUTATED MED12 WILD-TYPE 
              2               3 
$`MED12 MUTATED`
TCGA-F2-A44G TCGA-FB-A7DR TCGA-IB-7651 TCGA-IB-A5SO 
         153          166         1989          329 

$`MED12 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7925 
         360          449            1          396           28          361 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SP 
          11           13          476          851           17          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY 
        1991            8         1968          127          110          416 
TCGA-US-A776 
         844 

  MED12 MUTATED MED12 WILD-TYPE 
            153               1 
  MED12 MUTATED MED12 WILD-TYPE 
           1989            1991 
  MED12 MUTATED MED12 WILD-TYPE 
          247.5           360.0 
[1] "153.0 - 1989.0 (247.5)" "1.0 - 1991.0 (360.0)"  
[1] "hr=" "2.7"
D19V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MED12 MUTATED          0         1         4         0        0
  MED12 WILD-TYPE        2         5        19         1        1
D19V3, multiclass
           clus
vv          MED12 MUTATED MED12 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             4              19
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  MED12 MUTATED          5
  MED12 WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D19V5, binary
                 cls
clus               0  1
  MED12 MUTATED    0  4
  MED12 WILD-TYPE  7 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      0    4
  MED12 WILD-TYPE    7   21
   clus
vv  MED12 MUTATED MED12 WILD-TYPE
  0             0               7
  1             4              21
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  MED12 MUTATED    4  0  1
  MED12 WILD-TYPE 15  1 12
D19V6, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  M0             4              15
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                 cls
clus               0  1
  MED12 MUTATED    3  2
  MED12 WILD-TYPE 11 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      3    2
  MED12 WILD-TYPE   11   17
        clus
vv       MED12 MUTATED MED12 WILD-TYPE
  FEMALE             3              11
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MED12 MUTATED                                     4
  MED12 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MED12 MUTATED                                       0
  MED12 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MED12 MUTATED                                                  1
  MED12 WILD-TYPE                                                1
D19V8, multiclass
                                                  clus
vv                                                 MED12 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 MED12 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  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"
D19V9, continuous
[1] "Remove cluster labels:" "MED12 MUTATED"         
clus
  MED12 MUTATED MED12 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-H8-A6C1      TCGA-IB-7885 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" "MED12 WILD-TYPE" 
     TCGA-OE-A75W 
"MED12 WILD-TYPE" 
D19V10, binary
                 cls
clus               0  1
  MED12 MUTATED    4  1
  MED12 WILD-TYPE 20  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      4    1
  MED12 WILD-TYPE   20    8
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  R0             4              20
  R1             1               8
[1] 2 2
[1] FALSE
D19V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED12 MUTATED       1                         0     4
  MED12 WILD-TYPE     1                         3    24
D19V12, multiclass
                           clus
vv                          MED12 MUTATED MED12 WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = BMP2K MUTATION ANALYSIS
D20V1, survival
                 sevent
clus2              0  1
  BMP2K MUTATED    2  1
  BMP2K WILD-TYPE 16  4
  BMP2K MUTATED BMP2K WILD-TYPE 
              3              20 
  BMP2K MUTATED BMP2K WILD-TYPE 
              1               4 
$`BMP2K MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-A5SO 
         361         1989          329 

$`BMP2K WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28           11           13          476          851           17 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  BMP2K MUTATED BMP2K WILD-TYPE 
            329               1 
  BMP2K MUTATED BMP2K WILD-TYPE 
           1989            1991 
  BMP2K MUTATED BMP2K WILD-TYPE 
            361             233 
[1] "329.0 - 1989.0 (361.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.3"
D20V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BMP2K MUTATED          0         0         3         0        0
  BMP2K WILD-TYPE        2         6        20         1        1
D20V3, multiclass
           clus
vv          BMP2K MUTATED BMP2K WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  BMP2K MUTATED          3
  BMP2K WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D20V5, binary
                 cls
clus               0  1
  BMP2K MUTATED    0  3
  BMP2K WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      0    3
  BMP2K WILD-TYPE    7   22
   clus
vv  BMP2K MUTATED BMP2K WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  BMP2K MUTATED    2  0  1
  BMP2K WILD-TYPE 17  1 12
D20V6, multiclass
    clus
vv   BMP2K MUTATED BMP2K WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                 cls
clus               0  1
  BMP2K MUTATED    1  2
  BMP2K WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      1    2
  BMP2K WILD-TYPE   13   17
        clus
vv       BMP2K MUTATED BMP2K WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BMP2K MUTATED                                     3
  BMP2K WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BMP2K MUTATED                                       0
  BMP2K WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BMP2K MUTATED                                                  0
  BMP2K WILD-TYPE                                                2
D20V8, multiclass
                                                  clus
vv                                                 BMP2K MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 BMP2K WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, continuous
[1] "Remove cluster labels:" "BMP2K MUTATED"         
clus
  BMP2K MUTATED BMP2K WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
D20V10, binary
                 cls
clus               0  1
  BMP2K MUTATED    3  0
  BMP2K WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      3    0
  BMP2K WILD-TYPE   21    9
    clus
vv   BMP2K MUTATED BMP2K WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D20V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BMP2K MUTATED       0                         0     3
  BMP2K WILD-TYPE     2                         3    25
D20V12, multiclass
                           clus
vv                          BMP2K MUTATED BMP2K WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = ZMYM5 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2              0  1
  ZMYM5 MUTATED    2  1
  ZMYM5 WILD-TYPE 16  4
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
              3              20 
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
              1               4 
$`ZMYM5 MUTATED`
TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-IB-7651 
         396          361         1989 

$`ZMYM5 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
          11           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
            361               1 
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
           1989            1991 
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
            396             233 
[1] "361.0 - 1989.0 (396.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D21V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZMYM5 MUTATED          0         1         3         0        0
  ZMYM5 WILD-TYPE        2         5        20         1        1
D21V3, multiclass
           clus
vv          ZMYM5 MUTATED ZMYM5 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  ZMYM5 MUTATED          4
  ZMYM5 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D21V5, binary
                 cls
clus               0  1
  ZMYM5 MUTATED    1  3
  ZMYM5 WILD-TYPE  6 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM5 MUTATED      1    3
  ZMYM5 WILD-TYPE    6   22
   clus
vv  ZMYM5 MUTATED ZMYM5 WILD-TYPE
  0             1               6
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  ZMYM5 MUTATED    1  0  3
  ZMYM5 WILD-TYPE 18  1 10
D21V6, multiclass
    clus
vv   ZMYM5 MUTATED ZMYM5 WILD-TYPE
  M0             1              18
  M1             0               1
  MX             3              10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                 cls
clus               0  1
  ZMYM5 MUTATED    1  3
  ZMYM5 WILD-TYPE 13 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM5 MUTATED      1    3
  ZMYM5 WILD-TYPE   13   16
        clus
vv       ZMYM5 MUTATED ZMYM5 WILD-TYPE
  FEMALE             1              13
  MALE               3              16
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMYM5 MUTATED                                     3
  ZMYM5 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMYM5 MUTATED                                       1
  ZMYM5 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMYM5 MUTATED                                                  0
  ZMYM5 WILD-TYPE                                                2
D21V8, multiclass
                                                  clus
vv                                                 ZMYM5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ZMYM5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, continuous
[1] "Remove cluster labels:" "ZMYM5 MUTATED"         
clus
  ZMYM5 MUTATED ZMYM5 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-IB-7885 
"ZMYM5 WILD-TYPE" "ZMYM5 WILD-TYPE" "ZMYM5 WILD-TYPE" "ZMYM5 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"ZMYM5 WILD-TYPE" "ZMYM5 WILD-TYPE" "ZMYM5 WILD-TYPE" "ZMYM5 WILD-TYPE" 
     TCGA-OE-A75W 
"ZMYM5 WILD-TYPE" 
D21V10, binary
                 cls
clus               0  1
  ZMYM5 MUTATED    3  1
  ZMYM5 WILD-TYPE 21  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM5 MUTATED      3    1
  ZMYM5 WILD-TYPE   21    8
    clus
vv   ZMYM5 MUTATED ZMYM5 WILD-TYPE
  R0             3              21
  R1             1               8
[1] 2 2
[1] FALSE
D21V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM5 MUTATED       0                         0     4
  ZMYM5 WILD-TYPE     2                         3    24
D21V12, multiclass
                           clus
vv                          ZMYM5 MUTATED ZMYM5 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = SYT15 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2              0  1
  SYT15 MUTATED    1  2
  SYT15 WILD-TYPE 17  3
  SYT15 MUTATED SYT15 WILD-TYPE 
              3              20 
  SYT15 MUTATED SYT15 WILD-TYPE 
              2               3 
$`SYT15 MUTATED`
TCGA-F2-7273 TCGA-IB-7651 TCGA-US-A776 
         360         1989          844 

$`SYT15 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY 
         110          416 

  SYT15 MUTATED SYT15 WILD-TYPE 
            360               1 
  SYT15 MUTATED SYT15 WILD-TYPE 
           1989            1991 
  SYT15 MUTATED SYT15 WILD-TYPE 
            844             233 
[1] "360.0 - 1989.0 (844.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "2.2"
D22V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SYT15 MUTATED          0         1         2         0        0
  SYT15 WILD-TYPE        2         5        21         1        1
D22V3, multiclass
           clus
vv          SYT15 MUTATED SYT15 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  SYT15 MUTATED          3
  SYT15 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D22V5, binary
                 cls
clus               0  1
  SYT15 MUTATED    1  2
  SYT15 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT15 MUTATED      1    2
  SYT15 WILD-TYPE    6   23
   clus
vv  SYT15 MUTATED SYT15 WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  SYT15 MUTATED    2  0  1
  SYT15 WILD-TYPE 17  1 12
D22V6, multiclass
    clus
vv   SYT15 MUTATED SYT15 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                 cls
clus               0  1
  SYT15 MUTATED    1  2
  SYT15 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT15 MUTATED      1    2
  SYT15 WILD-TYPE   13   17
        clus
vv       SYT15 MUTATED SYT15 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYT15 MUTATED                                     2
  SYT15 WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYT15 MUTATED                                       0
  SYT15 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYT15 MUTATED                                                  1
  SYT15 WILD-TYPE                                                1
D22V8, multiclass
                                                  clus
vv                                                 SYT15 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 SYT15 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  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"
D22V9, continuous
[1] "Remove cluster labels:" "SYT15 MUTATED"         
clus
  SYT15 MUTATED SYT15 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"SYT15 WILD-TYPE" "SYT15 WILD-TYPE" "SYT15 WILD-TYPE" "SYT15 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"SYT15 WILD-TYPE" "SYT15 WILD-TYPE" "SYT15 WILD-TYPE" "SYT15 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"SYT15 WILD-TYPE" "SYT15 WILD-TYPE" 
D22V10, binary
                 cls
clus               0  1
  SYT15 MUTATED    2  1
  SYT15 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT15 MUTATED      2    1
  SYT15 WILD-TYPE   22    8
    clus
vv   SYT15 MUTATED SYT15 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D22V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYT15 MUTATED       0                         1     2
  SYT15 WILD-TYPE     2                         2    26
D22V12, multiclass
                           clus
vv                          SYT15 MUTATED SYT15 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 2              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = PLAU MUTATION ANALYSIS
D23V1, survival
                sevent
clus2             0  1
  PLAU MUTATED    1  2
  PLAU WILD-TYPE 17  3
  PLAU MUTATED PLAU WILD-TYPE 
             3             20 
  PLAU MUTATED PLAU WILD-TYPE 
             2              3 
$`PLAU MUTATED`
TCGA-F2-7273 TCGA-IB-7651 TCGA-IB-A5ST 
         360         1989            8 

$`PLAU WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         329          300         1991         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  PLAU MUTATED PLAU WILD-TYPE 
             8              1 
  PLAU MUTATED PLAU WILD-TYPE 
          1989           1991 
  PLAU MUTATED PLAU WILD-TYPE 
         360.0          314.5 
[1] "8.0 - 1989.0 (360.0)" "1.0 - 1991.0 (314.5)"
[1] "hr=" "2.8"
D23V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PLAU MUTATED          1         0         3         0        0
  PLAU WILD-TYPE        1         6        20         1        1
D23V3, multiclass
           clus
vv          PLAU MUTATED PLAU WILD-TYPE
  STAGE IB             1              1
  STAGE IIA            0              6
  STAGE IIB            3             20
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  PLAU MUTATED          4
  PLAU WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D23V5, binary
                cls
clus              0  1
  PLAU MUTATED    1  3
  PLAU WILD-TYPE  6 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLAU MUTATED      1    3
  PLAU WILD-TYPE    6   22
   clus
vv  PLAU MUTATED PLAU WILD-TYPE
  0            1              6
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  PLAU MUTATED    4  0  0
  PLAU WILD-TYPE 15  1 13
D23V6, multiclass
    clus
vv   PLAU MUTATED PLAU WILD-TYPE
  M0            4             15
  M1            0              1
  MX            0             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                cls
clus              0  1
  PLAU MUTATED    3  1
  PLAU WILD-TYPE 11 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLAU MUTATED      3    1
  PLAU WILD-TYPE   11   18
        clus
vv       PLAU MUTATED PLAU WILD-TYPE
  FEMALE            3             11
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PLAU MUTATED                                     4
  PLAU WILD-TYPE                                  24
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PLAU MUTATED                                       0
  PLAU WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PLAU MUTATED                                                  0
  PLAU WILD-TYPE                                                2
D23V8, multiclass
                                                  clus
vv                                                 PLAU MUTATED PLAU WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4             24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D23V9, continuous
[1] "Remove cluster labels:" "PLAU MUTATED"          
clus
  PLAU MUTATED PLAU WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"PLAU WILD-TYPE" "PLAU WILD-TYPE" "PLAU WILD-TYPE" "PLAU WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG 
"PLAU WILD-TYPE" "PLAU WILD-TYPE" "PLAU WILD-TYPE" "PLAU WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"PLAU WILD-TYPE" "PLAU WILD-TYPE" 
D23V10, binary
                cls
clus              0  1
  PLAU MUTATED    3  1
  PLAU WILD-TYPE 21  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLAU MUTATED      3    1
  PLAU WILD-TYPE   21    8
    clus
vv   PLAU MUTATED PLAU WILD-TYPE
  R0            3             21
  R1            1              8
[1] 2 2
[1] FALSE
D23V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PLAU MUTATED       0                         1     3
  PLAU WILD-TYPE     2                         2    25
D23V12, multiclass
                           clus
vv                          PLAU MUTATED PLAU WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = MEPCE MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2              0  1
  MEPCE MUTATED    2  1
  MEPCE WILD-TYPE 16  4
  MEPCE MUTATED MEPCE WILD-TYPE 
              3              20 
  MEPCE MUTATED MEPCE WILD-TYPE 
              1               4 
$`MEPCE MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-US-A776 
        1989          851          844 

$`MEPCE WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 
          28          361           11           13          476           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY 
         110          416 

  MEPCE MUTATED MEPCE WILD-TYPE 
            844               1 
  MEPCE MUTATED MEPCE WILD-TYPE 
           1989            1991 
  MEPCE MUTATED MEPCE WILD-TYPE 
            851             233 
[1] "844.0 - 1989.0 (851.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D24V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MEPCE MUTATED          0         1         2         0        0
  MEPCE WILD-TYPE        2         5        21         1        1
D24V3, multiclass
           clus
vv          MEPCE MUTATED MEPCE WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  MEPCE MUTATED          3
  MEPCE WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D24V5, binary
                 cls
clus               0  1
  MEPCE MUTATED    1  2
  MEPCE WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      1    2
  MEPCE WILD-TYPE    6   23
   clus
vv  MEPCE MUTATED MEPCE WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  MEPCE MUTATED    2  0  1
  MEPCE WILD-TYPE 17  1 12
D24V6, multiclass
    clus
vv   MEPCE MUTATED MEPCE WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                 cls
clus               0  1
  MEPCE MUTATED    2  1
  MEPCE WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      2    1
  MEPCE WILD-TYPE   12   18
        clus
vv       MEPCE MUTATED MEPCE WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MEPCE MUTATED                                     2
  MEPCE WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MEPCE MUTATED                                       0
  MEPCE WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MEPCE MUTATED                                                  1
  MEPCE WILD-TYPE                                                1
D24V8, multiclass
                                                  clus
vv                                                 MEPCE MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 MEPCE WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  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"
D24V9, continuous
[1] "Remove cluster labels:" "MEPCE MUTATED"         
clus
  MEPCE MUTATED MEPCE WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"MEPCE WILD-TYPE" "MEPCE WILD-TYPE" "MEPCE WILD-TYPE" "MEPCE WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"MEPCE WILD-TYPE" "MEPCE WILD-TYPE" "MEPCE WILD-TYPE" "MEPCE WILD-TYPE" 
     TCGA-OE-A75W 
"MEPCE WILD-TYPE" 
D24V10, binary
                 cls
clus               0  1
  MEPCE MUTATED    3  0
  MEPCE WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEPCE MUTATED      3    0
  MEPCE WILD-TYPE   21    9
    clus
vv   MEPCE MUTATED MEPCE WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D24V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MEPCE MUTATED       0                         0     3
  MEPCE WILD-TYPE     2                         3    25
D24V12, multiclass
                           clus
vv                          MEPCE MUTATED MEPCE WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = ZMIZ1 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2              0  1
  ZMIZ1 MUTATED    4  1
  ZMIZ1 WILD-TYPE 14  4
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              5              18 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              1               4 
$`ZMIZ1 MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-8126 TCGA-LB-A7SX 
         361         1989          851           17          127 

$`ZMIZ1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-A5SO TCGA-IB-A5SP 
          28           11           13          476          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
        1991            8         1968          110          416          844 

  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
             17               1 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
           1989            1991 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
          361.0           314.5 
[1] "17.0 - 1989.0 (361.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.5"
D25V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZMIZ1 MUTATED          0         0         4         1        0
  ZMIZ1 WILD-TYPE        2         6        19         0        1
D25V3, multiclass
           clus
vv          ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             4              19
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  ZMIZ1 MUTATED          5
  ZMIZ1 WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D25V5, binary
                 cls
clus               0  1
  ZMIZ1 MUTATED    0  5
  ZMIZ1 WILD-TYPE  7 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      0    5
  ZMIZ1 WILD-TYPE    7   20
   clus
vv  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  0             0               7
  1             5              20
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  ZMIZ1 MUTATED    3  0  2
  ZMIZ1 WILD-TYPE 16  1 11
D25V6, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                 cls
clus               0  1
  ZMIZ1 MUTATED    4  1
  ZMIZ1 WILD-TYPE 10 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      4    1
  ZMIZ1 WILD-TYPE   10   18
        clus
vv       ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  FEMALE             4              10
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZMIZ1 MUTATED                                     5
  ZMIZ1 WILD-TYPE                                  23
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZMIZ1 MUTATED                                       0
  ZMIZ1 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZMIZ1 MUTATED                                                  0
  ZMIZ1 WILD-TYPE                                                2
D25V8, multiclass
                                                  clus
vv                                                 ZMIZ1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ZMIZ1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, continuous
D25V10, binary
                 cls
clus               0  1
  ZMIZ1 MUTATED    3  2
  ZMIZ1 WILD-TYPE 21  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      3    2
  ZMIZ1 WILD-TYPE   21    7
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  R0             3              21
  R1             2               7
[1] 2 2
[1] FALSE
D25V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMIZ1 MUTATED       0                         1     4
  ZMIZ1 WILD-TYPE     2                         2    24
D25V12, multiclass
                           clus
vv                          ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = SLC39A5 MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                0  1
  SLC39A5 MUTATED    2  1
  SLC39A5 WILD-TYPE 16  4
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
                3                20 
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
                1                 4 
$`SLC39A5 MUTATED`
TCGA-HZ-7925 TCGA-IB-A6UG TCGA-Q3-A5QY 
         361         1968          416 

$`SLC39A5 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          28           11           13         1989          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-LB-A7SX 
          17          329          300         1991            8          127 
TCGA-OE-A75W TCGA-US-A776 
         110          844 

  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
              361                 1 
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
             1968              1991 
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
              416               233 
[1] "361.0 - 1968.0 (416.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.4"
D26V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SLC39A5 MUTATED          0         0         4         0        0
  SLC39A5 WILD-TYPE        2         6        19         1        1
D26V3, multiclass
           clus
vv          SLC39A5 MUTATED SLC39A5 WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               0                 6
  STAGE IIB               4                19
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  SLC39A5 MUTATED          4
  SLC39A5 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D26V5, binary
                   cls
clus                 0  1
  SLC39A5 MUTATED    0  4
  SLC39A5 WILD-TYPE  7 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A5 MUTATED      0    4
  SLC39A5 WILD-TYPE    7   21
   clus
vv  SLC39A5 MUTATED SLC39A5 WILD-TYPE
  0               0                 7
  1               4                21
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  SLC39A5 MUTATED    1  0  3
  SLC39A5 WILD-TYPE 18  1 10
D26V6, multiclass
    clus
vv   SLC39A5 MUTATED SLC39A5 WILD-TYPE
  M0               1                18
  M1               0                 1
  MX               3                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                   cls
clus                 0  1
  SLC39A5 MUTATED    1  3
  SLC39A5 WILD-TYPE 13 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A5 MUTATED      1    3
  SLC39A5 WILD-TYPE   13   16
        clus
vv       SLC39A5 MUTATED SLC39A5 WILD-TYPE
  FEMALE               1                13
  MALE                 3                16
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC39A5 MUTATED                                     4
  SLC39A5 WILD-TYPE                                  24
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC39A5 MUTATED                                       0
  SLC39A5 WILD-TYPE                                     3
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC39A5 MUTATED                                                  0
  SLC39A5 WILD-TYPE                                                2
D26V8, multiclass
                                                  clus
vv                                                 SLC39A5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 SLC39A5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, continuous
[1] "Remove cluster labels:" "SLC39A5 MUTATED"       
clus
  SLC39A5 MUTATED SLC39A5 WILD-TYPE 
                1                10 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-H8-A6C1 
"SLC39A5 WILD-TYPE" "SLC39A5 WILD-TYPE" "SLC39A5 WILD-TYPE" "SLC39A5 WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A5SS 
"SLC39A5 WILD-TYPE" "SLC39A5 WILD-TYPE" "SLC39A5 WILD-TYPE" "SLC39A5 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W 
"SLC39A5 WILD-TYPE" "SLC39A5 WILD-TYPE" 
D26V10, binary
                   cls
clus                 0  1
  SLC39A5 MUTATED    3  1
  SLC39A5 WILD-TYPE 21  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A5 MUTATED      3    1
  SLC39A5 WILD-TYPE   21    8
    clus
vv   SLC39A5 MUTATED SLC39A5 WILD-TYPE
  R0               3                21
  R1               1                 8
[1] 2 2
[1] FALSE
D26V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC39A5 MUTATED       0                         0     4
  SLC39A5 WILD-TYPE     2                         3    24
D26V12, multiclass
                           clus
vv                          SLC39A5 MUTATED SLC39A5 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   4                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = GUCY2F MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2               0  1
  GUCY2F MUTATED    3  2
  GUCY2F WILD-TYPE 15  3
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               5               18 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               2                3 
$`GUCY2F MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A6UG TCGA-Q3-A5QY 
        1989          851          329         1968          416 

$`GUCY2F WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 
          28          361           11           13          476           17 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-LB-A7SX TCGA-OE-A75W TCGA-US-A776 
         300         1991            8          127          110          844 

  GUCY2F MUTATED GUCY2F WILD-TYPE 
             329                1 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
            1989             1991 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
           851.0            159.5 
[1] "329.0 - 1989.0 (851.0)" "1.0 - 1991.0 (159.5)"  
[1] "hr=" "1.2"
D27V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GUCY2F MUTATED          0         0         5         0        0
  GUCY2F WILD-TYPE        2         6        18         1        1
D27V3, multiclass
           clus
vv          GUCY2F MUTATED GUCY2F WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              0                6
  STAGE IIB              5               18
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  GUCY2F MUTATED          5
  GUCY2F WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D27V5, binary
                  cls
clus                0  1
  GUCY2F MUTATED    0  5
  GUCY2F WILD-TYPE  7 20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      0    5
  GUCY2F WILD-TYPE    7   20
   clus
vv  GUCY2F MUTATED GUCY2F WILD-TYPE
  0              0                7
  1              5               20
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  GUCY2F MUTATED    4  0  1
  GUCY2F WILD-TYPE 15  1 12
D27V6, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  M0              4               15
  M1              0                1
  MX              1               12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                  cls
clus                0  1
  GUCY2F MUTATED    2  3
  GUCY2F WILD-TYPE 12 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      2    3
  GUCY2F WILD-TYPE   12   16
        clus
vv       GUCY2F MUTATED GUCY2F WILD-TYPE
  FEMALE              2               12
  MALE                3               16
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GUCY2F MUTATED                                     5
  GUCY2F WILD-TYPE                                  23
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GUCY2F MUTATED                                       0
  GUCY2F WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GUCY2F MUTATED                                                  0
  GUCY2F WILD-TYPE                                                2
D27V8, multiclass
                                                  clus
vv                                                 GUCY2F MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 GUCY2F WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, continuous
D27V10, binary
                  cls
clus                0  1
  GUCY2F MUTATED    4  1
  GUCY2F WILD-TYPE 20  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED      4    1
  GUCY2F WILD-TYPE   20    8
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  R0              4               20
  R1              1                8
[1] 2 2
[1] FALSE
D27V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GUCY2F MUTATED       0                         0     5
  GUCY2F WILD-TYPE     2                         3    23
D27V12, multiclass
                           clus
vv                          GUCY2F MUTATED GUCY2F WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  5               23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = EDC4 MUTATION ANALYSIS
D28V1, survival
                sevent
clus2             0  1
  EDC4 MUTATED    2  2
  EDC4 WILD-TYPE 16  3
  EDC4 MUTATED EDC4 WILD-TYPE 
             4             19 
  EDC4 MUTATED EDC4 WILD-TYPE 
             2              3 
$`EDC4 MUTATED`
TCGA-IB-7651 TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W 
        1989            8         1968          110 

$`EDC4 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-LB-A7SX TCGA-Q3-A5QY 
          17          329          300         1991          127          416 
TCGA-US-A776 
         844 

  EDC4 MUTATED EDC4 WILD-TYPE 
             8              1 
  EDC4 MUTATED EDC4 WILD-TYPE 
          1989           1991 
  EDC4 MUTATED EDC4 WILD-TYPE 
          1039            329 
[1] "8.0 - 1989.0 (1039.0)" "1.0 - 1991.0 (329.0)" 
[1] "hr=" "2"  
D28V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  EDC4 MUTATED          0         1         4         0        0
  EDC4 WILD-TYPE        2         5        19         1        1
D28V3, multiclass
           clus
vv          EDC4 MUTATED EDC4 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            1              5
  STAGE IIB            4             19
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  EDC4 MUTATED          5
  EDC4 WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D28V5, binary
                cls
clus              0  1
  EDC4 MUTATED    1  4
  EDC4 WILD-TYPE  6 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      1    4
  EDC4 WILD-TYPE    6   21
   clus
vv  EDC4 MUTATED EDC4 WILD-TYPE
  0            1              6
  1            4             21
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  EDC4 MUTATED    5  0  0
  EDC4 WILD-TYPE 14  1 13
D28V6, multiclass
    clus
vv   EDC4 MUTATED EDC4 WILD-TYPE
  M0            5             14
  M1            0              1
  MX            0             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                cls
clus              0  1
  EDC4 MUTATED    2  3
  EDC4 WILD-TYPE 12 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      2    3
  EDC4 WILD-TYPE   12   16
        clus
vv       EDC4 MUTATED EDC4 WILD-TYPE
  FEMALE            2             12
  MALE              3             16
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EDC4 MUTATED                                     5
  EDC4 WILD-TYPE                                  23
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EDC4 MUTATED                                       0
  EDC4 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EDC4 MUTATED                                                  0
  EDC4 WILD-TYPE                                                2
D28V8, multiclass
                                                  clus
vv                                                 EDC4 MUTATED EDC4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         5             23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D28V9, continuous
D28V10, binary
                cls
clus              0  1
  EDC4 MUTATED    4  1
  EDC4 WILD-TYPE 20  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      4    1
  EDC4 WILD-TYPE   20    8
    clus
vv   EDC4 MUTATED EDC4 WILD-TYPE
  R0            4             20
  R1            1              8
[1] 2 2
[1] FALSE
D28V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EDC4 MUTATED       0                         1     4
  EDC4 WILD-TYPE     2                         2    24
D28V12, multiclass
                           clus
vv                          EDC4 MUTATED EDC4 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                4             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = SEH1L MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2              0  1
  SEH1L MUTATED    2  1
  SEH1L WILD-TYPE 16  4
  SEH1L MUTATED SEH1L WILD-TYPE 
              3              20 
  SEH1L MUTATED SEH1L WILD-TYPE 
              1               4 
$`SEH1L MUTATED`
TCGA-HZ-7918 TCGA-HZ-A77P TCGA-IB-7651 
          28           13         1989 

$`SEH1L WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
         361           11          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  SEH1L MUTATED SEH1L WILD-TYPE 
             13               1 
  SEH1L MUTATED SEH1L WILD-TYPE 
           1989            1991 
  SEH1L MUTATED SEH1L WILD-TYPE 
           28.0           344.5 
[1] "13.0 - 1989.0 (28.0)" "1.0 - 1991.0 (344.5)"
[1] "hr=" "1"  
D29V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SEH1L MUTATED          0         0         3         0        0
  SEH1L WILD-TYPE        2         6        20         1        1
D29V3, multiclass
           clus
vv          SEH1L MUTATED SEH1L WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  SEH1L MUTATED          3
  SEH1L WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D29V5, binary
                 cls
clus               0  1
  SEH1L MUTATED    0  3
  SEH1L WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEH1L MUTATED      0    3
  SEH1L WILD-TYPE    7   22
   clus
vv  SEH1L MUTATED SEH1L WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  SEH1L MUTATED    2  0  1
  SEH1L WILD-TYPE 17  1 12
D29V6, multiclass
    clus
vv   SEH1L MUTATED SEH1L WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                 cls
clus               0  1
  SEH1L MUTATED    1  2
  SEH1L WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEH1L MUTATED      1    2
  SEH1L WILD-TYPE   13   17
        clus
vv       SEH1L MUTATED SEH1L WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SEH1L MUTATED                                     2
  SEH1L WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SEH1L MUTATED                                       1
  SEH1L WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SEH1L MUTATED                                                  0
  SEH1L WILD-TYPE                                                2
D29V8, multiclass
                                                  clus
vv                                                 SEH1L MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SEH1L WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, continuous
[1] "Remove cluster labels:" "SEH1L MUTATED"         
clus
  SEH1L MUTATED SEH1L WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"SEH1L WILD-TYPE" "SEH1L WILD-TYPE" 
D29V10, binary
                 cls
clus               0  1
  SEH1L MUTATED    3  0
  SEH1L WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEH1L MUTATED      3    0
  SEH1L WILD-TYPE   21    9
    clus
vv   SEH1L MUTATED SEH1L WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D29V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SEH1L MUTATED       0                         0     3
  SEH1L WILD-TYPE     2                         3    25
D29V12, multiclass
                           clus
vv                          SEH1L MUTATED SEH1L WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = SLC4A3 MUTATION ANALYSIS
D30V1, survival
                  sevent
clus2               0  1
  SLC4A3 MUTATED    2  1
  SLC4A3 WILD-TYPE 16  4
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               3               20 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               1                4 
$`SLC4A3 MUTATED`
TCGA-H8-A6C1 TCGA-IB-7651 TCGA-IB-7652 
         396         1989          476 

$`SLC4A3 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
         361           11           13          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
             396                1 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
            1989             1991 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
             476              233 
[1] "396.0 - 1989.0 (476.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D30V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SLC4A3 MUTATED          0         1         2         0        0
  SLC4A3 WILD-TYPE        2         5        21         1        1
D30V3, multiclass
           clus
vv          SLC4A3 MUTATED SLC4A3 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              1                5
  STAGE IIB              2               21
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  SLC4A3 MUTATED          3
  SLC4A3 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D30V5, binary
                  cls
clus                0  1
  SLC4A3 MUTATED    1  2
  SLC4A3 WILD-TYPE  6 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      1    2
  SLC4A3 WILD-TYPE    6   23
   clus
vv  SLC4A3 MUTATED SLC4A3 WILD-TYPE
  0              1                6
  1              2               23
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  SLC4A3 MUTATED    2  0  1
  SLC4A3 WILD-TYPE 17  1 12
D30V6, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  M0              2               17
  M1              0                1
  MX              1               12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                  cls
clus                0  1
  SLC4A3 MUTATED    2  1
  SLC4A3 WILD-TYPE 12 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      2    1
  SLC4A3 WILD-TYPE   12   18
        clus
vv       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  FEMALE              2               12
  MALE                1               18
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLC4A3 MUTATED                                     2
  SLC4A3 WILD-TYPE                                  26
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLC4A3 MUTATED                                       1
  SLC4A3 WILD-TYPE                                     2
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLC4A3 MUTATED                                                  0
  SLC4A3 WILD-TYPE                                                2
D30V8, multiclass
                                                  clus
vv                                                 SLC4A3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 SLC4A3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, continuous
[1] "Remove cluster labels:" "SLC4A3 MUTATED"        
clus
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-IB-7885 
"SLC4A3 WILD-TYPE" "SLC4A3 WILD-TYPE" "SLC4A3 WILD-TYPE" "SLC4A3 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-LB-A7SX 
"SLC4A3 WILD-TYPE" "SLC4A3 WILD-TYPE" "SLC4A3 WILD-TYPE" "SLC4A3 WILD-TYPE" 
      TCGA-OE-A75W 
"SLC4A3 WILD-TYPE" 
D30V10, binary
                  cls
clus                0  1
  SLC4A3 MUTATED    2  1
  SLC4A3 WILD-TYPE 22  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      2    1
  SLC4A3 WILD-TYPE   22    8
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  R0              2               22
  R1              1                8
[1] 2 2
[1] FALSE
D30V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC4A3 MUTATED       1                         0     2
  SLC4A3 WILD-TYPE     1                         3    26
D30V12, multiclass
                           clus
vv                          SLC4A3 MUTATED SLC4A3 WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  2               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = CD99L2 MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2               0  1
  CD99L2 MUTATED    2  0
  CD99L2 WILD-TYPE 16  5
  CD99L2 MUTATED CD99L2 WILD-TYPE 
               2               21 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
               0                5 
$`CD99L2 MUTATED`
TCGA-HZ-A77O TCGA-Q3-A5QY 
          11          416 

$`CD99L2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          28          361           13         1989          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-US-A776 
         127          110          844 

  CD99L2 MUTATED CD99L2 WILD-TYPE 
              11                1 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
             416             1991 
  CD99L2 MUTATED CD99L2 WILD-TYPE 
           213.5            329.0 
[1] "11.0 - 416.0 (213.5)" "1.0 - 1991.0 (329.0)"
[1] "Remove cluster labels:" "CD99L2 MUTATED"        
D31V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CD99L2 MUTATED          0         0         3         0        0
  CD99L2 WILD-TYPE        2         6        20         1        1
D31V3, multiclass
           clus
vv          CD99L2 MUTATED CD99L2 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              0                6
  STAGE IIB              3               20
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  CD99L2 MUTATED          3
  CD99L2 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D31V5, binary
                  cls
clus                0  1
  CD99L2 MUTATED    0  3
  CD99L2 WILD-TYPE  7 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      0    3
  CD99L2 WILD-TYPE    7   22
   clus
vv  CD99L2 MUTATED CD99L2 WILD-TYPE
  0              0                7
  1              3               22
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  CD99L2 MUTATED    0  0  3
  CD99L2 WILD-TYPE 19  1 10
D31V6, multiclass
    clus
vv   CD99L2 MUTATED CD99L2 WILD-TYPE
  M0              0               19
  M1              0                1
  MX              3               10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                  cls
clus                0  1
  CD99L2 MUTATED    2  1
  CD99L2 WILD-TYPE 12 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      2    1
  CD99L2 WILD-TYPE   12   18
        clus
vv       CD99L2 MUTATED CD99L2 WILD-TYPE
  FEMALE              2               12
  MALE                1               18
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CD99L2 MUTATED                                     3
  CD99L2 WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CD99L2 MUTATED                                       0
  CD99L2 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CD99L2 MUTATED                                                  0
  CD99L2 WILD-TYPE                                                2
D31V8, multiclass
                                                  clus
vv                                                 CD99L2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 CD99L2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, continuous
D31V10, binary
                  cls
clus                0  1
  CD99L2 MUTATED    3  0
  CD99L2 WILD-TYPE 21  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CD99L2 MUTATED      3    0
  CD99L2 WILD-TYPE   21    9
    clus
vv   CD99L2 MUTATED CD99L2 WILD-TYPE
  R0              3               21
  R1              0                9
[1] 2 2
[1] FALSE
D31V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD99L2 MUTATED       0                         0     3
  CD99L2 WILD-TYPE     2                         3    25
D31V12, multiclass
                           clus
vv                          CD99L2 MUTATED CD99L2 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = SBNO1 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2              0  1
  SBNO1 MUTATED    2  1
  SBNO1 WILD-TYPE 16  4
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              3              20 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              1               4 
$`SBNO1 MUTATED`
TCGA-H8-A6C1 TCGA-IB-A5SP TCGA-IB-A5SS 
         396          300         1991 

$`SBNO1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
         361           11           13         1989          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
          17          329            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  SBNO1 MUTATED SBNO1 WILD-TYPE 
            300               1 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
           1991            1989 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
          396.0           247.5 
[1] "300.0 - 1991.0 (396.0)" "1.0 - 1989.0 (247.5)"  
[1] "hr="   "1e+09"
D32V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SBNO1 MUTATED          0         2         1         0        0
  SBNO1 WILD-TYPE        2         4        22         1        1
D32V3, multiclass
           clus
vv          SBNO1 MUTATED SBNO1 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             2               4
  STAGE IIB             1              22
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  SBNO1 MUTATED          3
  SBNO1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D32V5, binary
                 cls
clus               0  1
  SBNO1 MUTATED    2  1
  SBNO1 WILD-TYPE  5 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      2    1
  SBNO1 WILD-TYPE    5   24
   clus
vv  SBNO1 MUTATED SBNO1 WILD-TYPE
  0             2               5
  1             1              24
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  SBNO1 MUTATED    2  0  1
  SBNO1 WILD-TYPE 17  1 12
D32V6, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                 cls
clus               0  1
  SBNO1 MUTATED    1  2
  SBNO1 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      1    2
  SBNO1 WILD-TYPE   13   17
        clus
vv       SBNO1 MUTATED SBNO1 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SBNO1 MUTATED                                     2
  SBNO1 WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SBNO1 MUTATED                                       1
  SBNO1 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SBNO1 MUTATED                                                  0
  SBNO1 WILD-TYPE                                                2
D32V8, multiclass
                                                  clus
vv                                                 SBNO1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SBNO1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, continuous
[1] "Remove cluster labels:" "SBNO1 MUTATED"         
clus
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-IB-7651 
"SBNO1 WILD-TYPE" "SBNO1 WILD-TYPE" "SBNO1 WILD-TYPE" "SBNO1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UG      TCGA-LB-A7SX 
"SBNO1 WILD-TYPE" "SBNO1 WILD-TYPE" "SBNO1 WILD-TYPE" "SBNO1 WILD-TYPE" 
     TCGA-OE-A75W 
"SBNO1 WILD-TYPE" 
D32V10, binary
                 cls
clus               0  1
  SBNO1 MUTATED    2  1
  SBNO1 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      2    1
  SBNO1 WILD-TYPE   22    8
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D32V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SBNO1 MUTATED       0                         0     3
  SBNO1 WILD-TYPE     2                         3    25
D32V12, multiclass
                           clus
vv                          SBNO1 MUTATED SBNO1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = NPNT MUTATION ANALYSIS
D33V1, survival
                sevent
clus2             0  1
  NPNT MUTATED    1  1
  NPNT WILD-TYPE 17  4
  NPNT MUTATED NPNT WILD-TYPE 
             2             21 
  NPNT MUTATED NPNT WILD-TYPE 
             1              4 
$`NPNT MUTATED`
TCGA-F2-A44G TCGA-Q3-A5QY 
         153          416 

$`NPNT WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
         361           11           13         1989          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-US-A776 
         127          110          844 

  NPNT MUTATED NPNT WILD-TYPE 
           153              1 
  NPNT MUTATED NPNT WILD-TYPE 
           416           1991 
  NPNT MUTATED NPNT WILD-TYPE 
         284.5          329.0 
[1] "153.0 - 416.0 (284.5)" "1.0 - 1991.0 (329.0)" 
[1] "Remove cluster labels:" "NPNT MUTATED"          
D33V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NPNT MUTATED          1         0         2         0        0
  NPNT WILD-TYPE        1         6        21         1        1
D33V3, multiclass
           clus
vv          NPNT MUTATED NPNT WILD-TYPE
  STAGE IB             1              1
  STAGE IIA            0              6
  STAGE IIB            2             21
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  NPNT MUTATED          3
  NPNT WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D33V5, binary
                cls
clus              0  1
  NPNT MUTATED    1  2
  NPNT WILD-TYPE  6 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPNT MUTATED      1    2
  NPNT WILD-TYPE    6   23
   clus
vv  NPNT MUTATED NPNT WILD-TYPE
  0            1              6
  1            2             23
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  NPNT MUTATED    2  0  1
  NPNT WILD-TYPE 17  1 12
D33V6, multiclass
    clus
vv   NPNT MUTATED NPNT WILD-TYPE
  M0            2             17
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                cls
clus              0  1
  NPNT MUTATED    2  1
  NPNT WILD-TYPE 12 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPNT MUTATED      2    1
  NPNT WILD-TYPE   12   18
        clus
vv       NPNT MUTATED NPNT WILD-TYPE
  FEMALE            2             12
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NPNT MUTATED                                     3
  NPNT WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NPNT MUTATED                                       0
  NPNT WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NPNT MUTATED                                                  0
  NPNT WILD-TYPE                                                2
D33V8, multiclass
                                                  clus
vv                                                 NPNT MUTATED NPNT WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D33V9, continuous
D33V10, binary
                cls
clus              0  1
  NPNT MUTATED    2  1
  NPNT WILD-TYPE 22  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPNT MUTATED      2    1
  NPNT WILD-TYPE   22    8
    clus
vv   NPNT MUTATED NPNT WILD-TYPE
  R0            2             22
  R1            1              8
[1] 2 2
[1] FALSE
D33V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NPNT MUTATED       0                         0     3
  NPNT WILD-TYPE     2                         3    25
D33V12, multiclass
                           clus
vv                          NPNT MUTATED NPNT WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = TMEM175 MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  TMEM175 MUTATED    3  1
  TMEM175 WILD-TYPE 15  4
  TMEM175 MUTATED TMEM175 WILD-TYPE 
                4                19 
  TMEM175 MUTATED TMEM175 WILD-TYPE 
                1                 4 
$`TMEM175 MUTATED`
TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-7885 TCGA-US-A776 
          11         1989          851          844 

$`TMEM175 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO 
          28          361           13          476           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY 
         416 

  TMEM175 MUTATED TMEM175 WILD-TYPE 
               11                 1 
  TMEM175 MUTATED TMEM175 WILD-TYPE 
             1989              1991 
  TMEM175 MUTATED TMEM175 WILD-TYPE 
            847.5             300.0 
[1] "11.0 - 1989.0 (847.5)" "1.0 - 1991.0 (300.0)" 
[1] "hr=" "1.5"
D34V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TMEM175 MUTATED          0         1         3         0        0
  TMEM175 WILD-TYPE        2         5        20         1        1
D34V3, multiclass
           clus
vv          TMEM175 MUTATED TMEM175 WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               1                 5
  STAGE IIB               3                20
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  TMEM175 MUTATED          4
  TMEM175 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D34V5, binary
                   cls
clus                 0  1
  TMEM175 MUTATED    1  3
  TMEM175 WILD-TYPE  6 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM175 MUTATED      1    3
  TMEM175 WILD-TYPE    6   22
   clus
vv  TMEM175 MUTATED TMEM175 WILD-TYPE
  0               1                 6
  1               3                22
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  TMEM175 MUTATED    2  0  2
  TMEM175 WILD-TYPE 17  1 11
D34V6, multiclass
    clus
vv   TMEM175 MUTATED TMEM175 WILD-TYPE
  M0               2                17
  M1               0                 1
  MX               2                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                   cls
clus                 0  1
  TMEM175 MUTATED    3  1
  TMEM175 WILD-TYPE 11 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM175 MUTATED      3    1
  TMEM175 WILD-TYPE   11   18
        clus
vv       TMEM175 MUTATED TMEM175 WILD-TYPE
  FEMALE               3                11
  MALE                 1                18
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMEM175 MUTATED                                     3
  TMEM175 WILD-TYPE                                  25
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMEM175 MUTATED                                       0
  TMEM175 WILD-TYPE                                     3
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMEM175 MUTATED                                                  1
  TMEM175 WILD-TYPE                                                1
D34V8, multiclass
                                                  clus
vv                                                 TMEM175 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 TMEM175 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            3
  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"
D34V9, continuous
[1] "Remove cluster labels:" "TMEM175 MUTATED"       
clus
  TMEM175 MUTATED TMEM175 WILD-TYPE 
                2                 9 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-H8-A6C1 
"TMEM175 WILD-TYPE" "TMEM175 WILD-TYPE" "TMEM175 WILD-TYPE" "TMEM175 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-LB-A7SX 
"TMEM175 WILD-TYPE" "TMEM175 WILD-TYPE" "TMEM175 WILD-TYPE" "TMEM175 WILD-TYPE" 
       TCGA-OE-A75W 
"TMEM175 WILD-TYPE" 
D34V10, binary
                   cls
clus                 0  1
  TMEM175 MUTATED    4  0
  TMEM175 WILD-TYPE 20  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM175 MUTATED      4    0
  TMEM175 WILD-TYPE   20    9
    clus
vv   TMEM175 MUTATED TMEM175 WILD-TYPE
  R0               4                20
  R1               0                 9
[1] 2 2
[1] FALSE
D34V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM175 MUTATED       0                         0     4
  TMEM175 WILD-TYPE     2                         3    24
D34V12, multiclass
                           clus
vv                          TMEM175 MUTATED TMEM175 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   4                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = IRX4 MUTATION ANALYSIS
D35V1, survival
                sevent
clus2             0  1
  IRX4 MUTATED    0  1
  IRX4 WILD-TYPE 18  4
  IRX4 MUTATED IRX4 WILD-TYPE 
             1             22 
  IRX4 MUTATED IRX4 WILD-TYPE 
             1              4 
$`IRX4 MUTATED`
TCGA-F2-A44G 
         153 

$`IRX4 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
         361           11           13         1989          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         127          110          416          844 

  IRX4 MUTATED IRX4 WILD-TYPE 
           153              1 
  IRX4 MUTATED IRX4 WILD-TYPE 
           153           1991 
  IRX4 MUTATED IRX4 WILD-TYPE 
         153.0          344.5 
[1] "153.0 - 153.0 (153.0)" "1.0 - 1991.0 (344.5)" 
[1] "Remove cluster labels:" "IRX4 MUTATED"          
D35V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  IRX4 MUTATED          0         0         3         0        0
  IRX4 WILD-TYPE        2         6        20         1        1
D35V3, multiclass
           clus
vv          IRX4 MUTATED IRX4 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            3             20
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  IRX4 MUTATED          3
  IRX4 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D35V5, binary
                cls
clus              0  1
  IRX4 MUTATED    0  3
  IRX4 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      0    3
  IRX4 WILD-TYPE    7   22
   clus
vv  IRX4 MUTATED IRX4 WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  IRX4 MUTATED    1  0  2
  IRX4 WILD-TYPE 18  1 11
D35V6, multiclass
    clus
vv   IRX4 MUTATED IRX4 WILD-TYPE
  M0            1             18
  M1            0              1
  MX            2             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                cls
clus              0  1
  IRX4 MUTATED    3  0
  IRX4 WILD-TYPE 11 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      3    0
  IRX4 WILD-TYPE   11   19
        clus
vv       IRX4 MUTATED IRX4 WILD-TYPE
  FEMALE            3             11
  MALE              0             19
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IRX4 MUTATED                                     3
  IRX4 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IRX4 MUTATED                                       0
  IRX4 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IRX4 MUTATED                                                  0
  IRX4 WILD-TYPE                                                2
D35V8, multiclass
                                                  clus
vv                                                 IRX4 MUTATED IRX4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D35V9, continuous
D35V10, binary
                cls
clus              0  1
  IRX4 MUTATED    2  1
  IRX4 WILD-TYPE 22  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRX4 MUTATED      2    1
  IRX4 WILD-TYPE   22    8
    clus
vv   IRX4 MUTATED IRX4 WILD-TYPE
  R0            2             22
  R1            1              8
[1] 2 2
[1] FALSE
D35V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRX4 MUTATED       0                         0     3
  IRX4 WILD-TYPE     2                         3    25
D35V12, multiclass
                           clus
vv                          IRX4 MUTATED IRX4 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = CLCC1 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2              0  1
  CLCC1 MUTATED    1  1
  CLCC1 WILD-TYPE 17  4
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              2              21 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              1               4 
$`CLCC1 MUTATED`
TCGA-F2-7273 TCGA-IB-7885 
         360          851 

$`CLCC1 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-8126 
         361           11           13         1989          476           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  CLCC1 MUTATED CLCC1 WILD-TYPE 
            360               1 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
            851            1991 
  CLCC1 MUTATED CLCC1 WILD-TYPE 
          605.5           300.0 
[1] "360.0 - 851.0 (605.5)" "1.0 - 1991.0 (300.0)" 
[1] "Remove cluster labels:" "CLCC1 MUTATED"         
D36V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CLCC1 MUTATED          0         0         3         0        0
  CLCC1 WILD-TYPE        2         6        20         1        1
D36V3, multiclass
           clus
vv          CLCC1 MUTATED CLCC1 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  CLCC1 MUTATED          3
  CLCC1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D36V5, binary
                 cls
clus               0  1
  CLCC1 MUTATED    0  3
  CLCC1 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      0    3
  CLCC1 WILD-TYPE    7   22
   clus
vv  CLCC1 MUTATED CLCC1 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  CLCC1 MUTATED    2  0  1
  CLCC1 WILD-TYPE 17  1 12
D36V6, multiclass
    clus
vv   CLCC1 MUTATED CLCC1 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                 cls
clus               0  1
  CLCC1 MUTATED    2  1
  CLCC1 WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      2    1
  CLCC1 WILD-TYPE   12   18
        clus
vv       CLCC1 MUTATED CLCC1 WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CLCC1 MUTATED                                     3
  CLCC1 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CLCC1 MUTATED                                       0
  CLCC1 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CLCC1 MUTATED                                                  0
  CLCC1 WILD-TYPE                                                2
D36V8, multiclass
                                                  clus
vv                                                 CLCC1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CLCC1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, continuous
[1] "Remove cluster labels:" "CLCC1 MUTATED"         
clus
  CLCC1 MUTATED CLCC1 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"CLCC1 WILD-TYPE" "CLCC1 WILD-TYPE" 
D36V10, binary
                 cls
clus               0  1
  CLCC1 MUTATED    2  1
  CLCC1 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCC1 MUTATED      2    1
  CLCC1 WILD-TYPE   22    8
    clus
vv   CLCC1 MUTATED CLCC1 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D36V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CLCC1 MUTATED       0                         1     2
  CLCC1 WILD-TYPE     2                         2    26
D36V12, multiclass
                           clus
vv                          CLCC1 MUTATED CLCC1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 2              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = BTNL8 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2              0  1
  BTNL8 MUTATED    3  1
  BTNL8 WILD-TYPE 15  4
  BTNL8 MUTATED BTNL8 WILD-TYPE 
              4              19 
  BTNL8 MUTATED BTNL8 WILD-TYPE 
              1               4 
$`BTNL8 MUTATED`
TCGA-FB-A78T TCGA-IB-7651 TCGA-IB-8126 TCGA-IB-A5SP 
           1         1989           17          300 

$`BTNL8 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
         361           11           13          476          851          329 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY 
        1991            8         1968          127          110          416 
TCGA-US-A776 
         844 

  BTNL8 MUTATED BTNL8 WILD-TYPE 
              1               8 
  BTNL8 MUTATED BTNL8 WILD-TYPE 
           1989            1991 
  BTNL8 MUTATED BTNL8 WILD-TYPE 
          158.5           360.0 
[1] "1.0 - 1989.0 (158.5)" "8.0 - 1991.0 (360.0)"
[1] "hr=" "1.1"
D37V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BTNL8 MUTATED          0         1         2         1        0
  BTNL8 WILD-TYPE        2         5        21         0        1
D37V3, multiclass
           clus
vv          BTNL8 MUTATED BTNL8 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  BTNL8 MUTATED          4
  BTNL8 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D37V5, binary
                 cls
clus               0  1
  BTNL8 MUTATED    1  3
  BTNL8 WILD-TYPE  6 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL8 MUTATED      1    3
  BTNL8 WILD-TYPE    6   22
   clus
vv  BTNL8 MUTATED BTNL8 WILD-TYPE
  0             1               6
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  BTNL8 MUTATED    4  0  0
  BTNL8 WILD-TYPE 15  1 13
D37V6, multiclass
    clus
vv   BTNL8 MUTATED BTNL8 WILD-TYPE
  M0             4              15
  M1             0               1
  MX             0              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                 cls
clus               0  1
  BTNL8 MUTATED    3  1
  BTNL8 WILD-TYPE 11 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL8 MUTATED      3    1
  BTNL8 WILD-TYPE   11   18
        clus
vv       BTNL8 MUTATED BTNL8 WILD-TYPE
  FEMALE             3              11
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BTNL8 MUTATED                                     4
  BTNL8 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BTNL8 MUTATED                                       0
  BTNL8 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BTNL8 MUTATED                                                  0
  BTNL8 WILD-TYPE                                                2
D37V8, multiclass
                                                  clus
vv                                                 BTNL8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 BTNL8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, continuous
D37V10, binary
                 cls
clus               0  1
  BTNL8 MUTATED    2  2
  BTNL8 WILD-TYPE 22  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL8 MUTATED      2    2
  BTNL8 WILD-TYPE   22    7
    clus
vv   BTNL8 MUTATED BTNL8 WILD-TYPE
  R0             2              22
  R1             2               7
[1] 2 2
[1] FALSE
D37V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BTNL8 MUTATED       0                         0     4
  BTNL8 WILD-TYPE     2                         3    24
D37V12, multiclass
                           clus
vv                          BTNL8 MUTATED BTNL8 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = SYNGAP1 MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  SYNGAP1 MUTATED    2  2
  SYNGAP1 WILD-TYPE 16  3
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
                4                19 
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
                2                 3 
$`SYNGAP1 MUTATED`
TCGA-F2-7273 TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7885 
         360           13         1989          851 

$`SYNGAP1 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
         361           11          476           17          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY 
        1991            8         1968          127          110          416 
TCGA-US-A776 
         844 

  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
               13                 1 
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
             1989              1991 
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
            605.5             300.0 
[1] "13.0 - 1989.0 (605.5)" "1.0 - 1991.0 (300.0)" 
[1] "hr=" "2.2"
D38V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SYNGAP1 MUTATED          0         0         4         0        0
  SYNGAP1 WILD-TYPE        2         6        19         1        1
D38V3, multiclass
           clus
vv          SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               0                 6
  STAGE IIB               4                19
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  SYNGAP1 MUTATED          4
  SYNGAP1 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D38V5, binary
                   cls
clus                 0  1
  SYNGAP1 MUTATED    0  4
  SYNGAP1 WILD-TYPE  7 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNGAP1 MUTATED      0    4
  SYNGAP1 WILD-TYPE    7   21
   clus
vv  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  0               0                 7
  1               4                21
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  SYNGAP1 MUTATED    3  0  1
  SYNGAP1 WILD-TYPE 16  1 12
D38V6, multiclass
    clus
vv   SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  M0               3                16
  M1               0                 1
  MX               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                   cls
clus                 0  1
  SYNGAP1 MUTATED    2  2
  SYNGAP1 WILD-TYPE 12 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNGAP1 MUTATED      2    2
  SYNGAP1 WILD-TYPE   12   17
        clus
vv       SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  FEMALE               2                12
  MALE                 2                17
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SYNGAP1 MUTATED                                     3
  SYNGAP1 WILD-TYPE                                  25
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SYNGAP1 MUTATED                                       1
  SYNGAP1 WILD-TYPE                                     2
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SYNGAP1 MUTATED                                                  0
  SYNGAP1 WILD-TYPE                                                2
D38V8, multiclass
                                                  clus
vv                                                 SYNGAP1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 SYNGAP1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, continuous
[1] "Remove cluster labels:" "SYNGAP1 MUTATED"       
clus
  SYNGAP1 MUTATED SYNGAP1 WILD-TYPE 
                2                 9 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-H8-A6C1 
"SYNGAP1 WILD-TYPE" "SYNGAP1 WILD-TYPE" "SYNGAP1 WILD-TYPE" "SYNGAP1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-LB-A7SX 
"SYNGAP1 WILD-TYPE" "SYNGAP1 WILD-TYPE" "SYNGAP1 WILD-TYPE" "SYNGAP1 WILD-TYPE" 
       TCGA-OE-A75W 
"SYNGAP1 WILD-TYPE" 
D38V10, binary
                   cls
clus                 0  1
  SYNGAP1 MUTATED    3  1
  SYNGAP1 WILD-TYPE 21  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNGAP1 MUTATED      3    1
  SYNGAP1 WILD-TYPE   21    8
    clus
vv   SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  R0               3                21
  R1               1                 8
[1] 2 2
[1] FALSE
D38V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SYNGAP1 MUTATED       0                         1     3
  SYNGAP1 WILD-TYPE     2                         2    25
D38V12, multiclass
                           clus
vv                          SYNGAP1 MUTATED SYNGAP1 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                   3                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = F8 MUTATION ANALYSIS
D39V1, survival
              sevent
clus2           0  1
  F8 MUTATED    1  1
  F8 WILD-TYPE 17  4
  F8 MUTATED F8 WILD-TYPE 
           2           21 
  F8 MUTATED F8 WILD-TYPE 
           1            4 
$`F8 MUTATED`
TCGA-IB-7651 TCGA-OE-A75W 
        1989          110 

$`F8 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-Q3-A5QY TCGA-US-A776 
         127          416          844 

  F8 MUTATED F8 WILD-TYPE 
         110            1 
  F8 MUTATED F8 WILD-TYPE 
        1989         1991 
  F8 MUTATED F8 WILD-TYPE 
      1049.5        329.0 
[1] "110.0 - 1989.0 (1049.5)" "1.0 - 1991.0 (329.0)"   
[1] "Remove cluster labels:" "F8 MUTATED"            
D39V2, continuous
              vv
clus           STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  F8 MUTATED          0         1         2         0        0
  F8 WILD-TYPE        2         5        21         1        1
D39V3, multiclass
           clus
vv          F8 MUTATED F8 WILD-TYPE
  STAGE IB           0            2
  STAGE IIA          1            5
  STAGE IIB          2           21
  STAGE III          0            1
  STAGE IV           0            1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           T2+T3+T4
  F8 MUTATED          3
  F8 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D39V5, binary
              cls
clus            0  1
  F8 MUTATED    1  2
  F8 WILD-TYPE  6 23
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      1    2
  F8 WILD-TYPE    6   23
   clus
vv  F8 MUTATED F8 WILD-TYPE
  0          1            6
  1          2           23
[1] 2 2
[1] FALSE
              vv
clus           M0 M1 MX
  F8 MUTATED    2  0  1
  F8 WILD-TYPE 17  1 12
D39V6, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  M0          2           17
  M1          0            1
  MX          1           12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
              cls
clus            0  1
  F8 MUTATED    1  2
  F8 WILD-TYPE 13 17
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      1    2
  F8 WILD-TYPE   13   17
        clus
vv       F8 MUTATED F8 WILD-TYPE
  FEMALE          1           13
  MALE            2           17
[1] 2 2
[1] FALSE
              vv
clus           PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  F8 MUTATED                                     3
  F8 WILD-TYPE                                  25
              vv
clus           PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  F8 MUTATED                                       0
  F8 WILD-TYPE                                     3
              vv
clus           PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  F8 MUTATED                                                  0
  F8 WILD-TYPE                                                2
D39V8, multiclass
                                                  clus
vv                                                 F8 MUTATED F8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                       3           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                     0            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"
D39V9, continuous
[1] "Remove cluster labels:" "F8 MUTATED"            
clus
  F8 MUTATED F8 WILD-TYPE 
           2            9 
  TCGA-FB-A5VM   TCGA-FB-A78T   TCGA-FB-A7DR   TCGA-H8-A6C1   TCGA-IB-7885 
"F8 WILD-TYPE" "F8 WILD-TYPE" "F8 WILD-TYPE" "F8 WILD-TYPE" "F8 WILD-TYPE" 
  TCGA-IB-8126   TCGA-IB-A5SS   TCGA-IB-A6UG   TCGA-LB-A7SX 
"F8 WILD-TYPE" "F8 WILD-TYPE" "F8 WILD-TYPE" "F8 WILD-TYPE" 
D39V10, binary
              cls
clus            0  1
  F8 MUTATED    3  0
  F8 WILD-TYPE 21  9
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED      3    0
  F8 WILD-TYPE   21    9
    clus
vv   F8 MUTATED F8 WILD-TYPE
  R0          3           21
  R1          0            9
[1] 2 2
[1] FALSE
D39V11, continuous
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  F8 MUTATED       0                         0     3
  F8 WILD-TYPE     2                         3    25
D39V12, multiclass
                           clus
vv                          F8 MUTATED F8 WILD-TYPE
  ASIAN                              0            2
  BLACK OR AFRICAN AMERICAN          0            3
  WHITE                              3           25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = SORBS2 MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2               0  1
  SORBS2 MUTATED    2  1
  SORBS2 WILD-TYPE 16  4
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               3               20 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
               1                4 
$`SORBS2 MUTATED`
TCGA-FB-A7DR TCGA-IB-7651 TCGA-IB-7885 
         166         1989          851 

$`SORBS2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449            1          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO 
         361           11           13          476           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  SORBS2 MUTATED SORBS2 WILD-TYPE 
             166                1 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
            1989             1991 
  SORBS2 MUTATED SORBS2 WILD-TYPE 
           851.0            314.5 
[1] "166.0 - 1989.0 (851.0)" "1.0 - 1991.0 (314.5)"  
[1] "hr=" "1.3"
D40V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SORBS2 MUTATED          1         1         2         0        0
  SORBS2 WILD-TYPE        1         5        21         1        1
D40V3, multiclass
           clus
vv          SORBS2 MUTATED SORBS2 WILD-TYPE
  STAGE IB               1                1
  STAGE IIA              1                5
  STAGE IIB              2               21
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  SORBS2 MUTATED          4
  SORBS2 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D40V5, binary
                  cls
clus                0  1
  SORBS2 MUTATED    1  2
  SORBS2 WILD-TYPE  6 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      1    2
  SORBS2 WILD-TYPE    6   23
   clus
vv  SORBS2 MUTATED SORBS2 WILD-TYPE
  0              1                6
  1              2               23
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  SORBS2 MUTATED    4  0  0
  SORBS2 WILD-TYPE 15  1 13
D40V6, multiclass
    clus
vv   SORBS2 MUTATED SORBS2 WILD-TYPE
  M0              4               15
  M1              0                1
  MX              0               13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                  cls
clus                0  1
  SORBS2 MUTATED    3  1
  SORBS2 WILD-TYPE 11 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      3    1
  SORBS2 WILD-TYPE   11   18
        clus
vv       SORBS2 MUTATED SORBS2 WILD-TYPE
  FEMALE              3               11
  MALE                1               18
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SORBS2 MUTATED                                     3
  SORBS2 WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SORBS2 MUTATED                                       0
  SORBS2 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SORBS2 MUTATED                                                  1
  SORBS2 WILD-TYPE                                                1
D40V8, multiclass
                                                  clus
vv                                                 SORBS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
                                                  clus
vv                                                 SORBS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  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"
D40V9, continuous
D40V10, binary
                  cls
clus                0  1
  SORBS2 MUTATED    4  0
  SORBS2 WILD-TYPE 20  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS2 MUTATED      4    0
  SORBS2 WILD-TYPE   20    9
    clus
vv   SORBS2 MUTATED SORBS2 WILD-TYPE
  R0              4               20
  R1              0                9
[1] 2 2
[1] FALSE
D40V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SORBS2 MUTATED       1                         0     3
  SORBS2 WILD-TYPE     1                         3    25
D40V12, multiclass
                           clus
vv                          SORBS2 MUTATED SORBS2 WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = NR4A3 MUTATION ANALYSIS
D41V1, survival
                 sevent
clus2              0  1
  NR4A3 MUTATED    2  1
  NR4A3 WILD-TYPE 16  4
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              3              20 
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              1               4 
$`NR4A3 MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-US-A776 
         361         1989          844 

$`NR4A3 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY 
         110          416 

  NR4A3 MUTATED NR4A3 WILD-TYPE 
            361               1 
  NR4A3 MUTATED NR4A3 WILD-TYPE 
           1989            1991 
  NR4A3 MUTATED NR4A3 WILD-TYPE 
            844             233 
[1] "361.0 - 1989.0 (844.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D41V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NR4A3 MUTATED          0         1         2         0        0
  NR4A3 WILD-TYPE        2         5        21         1        1
D41V3, multiclass
           clus
vv          NR4A3 MUTATED NR4A3 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  NR4A3 MUTATED          3
  NR4A3 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D41V5, binary
                 cls
clus               0  1
  NR4A3 MUTATED    1  2
  NR4A3 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A3 MUTATED      1    2
  NR4A3 WILD-TYPE    6   23
   clus
vv  NR4A3 MUTATED NR4A3 WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  NR4A3 MUTATED    1  0  2
  NR4A3 WILD-TYPE 18  1 11
D41V6, multiclass
    clus
vv   NR4A3 MUTATED NR4A3 WILD-TYPE
  M0             1              18
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                 cls
clus               0  1
  NR4A3 MUTATED    1  2
  NR4A3 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A3 MUTATED      1    2
  NR4A3 WILD-TYPE   13   17
        clus
vv       NR4A3 MUTATED NR4A3 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NR4A3 MUTATED                                     2
  NR4A3 WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NR4A3 MUTATED                                       0
  NR4A3 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NR4A3 MUTATED                                                  1
  NR4A3 WILD-TYPE                                                1
D41V8, multiclass
                                                  clus
vv                                                 NR4A3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 NR4A3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  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"
D41V9, continuous
[1] "Remove cluster labels:" "NR4A3 MUTATED"         
clus
  NR4A3 MUTATED NR4A3 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"NR4A3 WILD-TYPE" "NR4A3 WILD-TYPE" 
D41V10, binary
                 cls
clus               0  1
  NR4A3 MUTATED    3  0
  NR4A3 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A3 MUTATED      3    0
  NR4A3 WILD-TYPE   21    9
    clus
vv   NR4A3 MUTATED NR4A3 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D41V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NR4A3 MUTATED       0                         0     3
  NR4A3 WILD-TYPE     2                         3    25
D41V12, multiclass
                           clus
vv                          NR4A3 MUTATED NR4A3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = ZNF337 MUTATION ANALYSIS
D42V1, survival
                  sevent
clus2               0  1
  ZNF337 MUTATED    2  1
  ZNF337 WILD-TYPE 16  4
  ZNF337 MUTATED ZNF337 WILD-TYPE 
               3               20 
  ZNF337 MUTATED ZNF337 WILD-TYPE 
               1                4 
$`ZNF337 MUTATED`
TCGA-H8-A6C1 TCGA-IB-7651 TCGA-IB-7652 
         396         1989          476 

$`ZNF337 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
         361           11           13          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  ZNF337 MUTATED ZNF337 WILD-TYPE 
             396                1 
  ZNF337 MUTATED ZNF337 WILD-TYPE 
            1989             1991 
  ZNF337 MUTATED ZNF337 WILD-TYPE 
             476              233 
[1] "396.0 - 1989.0 (476.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D42V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZNF337 MUTATED          0         1         3         0        0
  ZNF337 WILD-TYPE        2         5        20         1        1
D42V3, multiclass
           clus
vv          ZNF337 MUTATED ZNF337 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              1                5
  STAGE IIB              3               20
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  ZNF337 MUTATED          4
  ZNF337 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D42V5, binary
                  cls
clus                0  1
  ZNF337 MUTATED    1  3
  ZNF337 WILD-TYPE  6 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF337 MUTATED      1    3
  ZNF337 WILD-TYPE    6   22
   clus
vv  ZNF337 MUTATED ZNF337 WILD-TYPE
  0              1                6
  1              3               22
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  ZNF337 MUTATED    2  0  2
  ZNF337 WILD-TYPE 17  1 11
D42V6, multiclass
    clus
vv   ZNF337 MUTATED ZNF337 WILD-TYPE
  M0              2               17
  M1              0                1
  MX              2               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                  cls
clus                0  1
  ZNF337 MUTATED    2  2
  ZNF337 WILD-TYPE 12 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF337 MUTATED      2    2
  ZNF337 WILD-TYPE   12   17
        clus
vv       ZNF337 MUTATED ZNF337 WILD-TYPE
  FEMALE              2               12
  MALE                2               17
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF337 MUTATED                                     3
  ZNF337 WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF337 MUTATED                                       1
  ZNF337 WILD-TYPE                                     2
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF337 MUTATED                                                  0
  ZNF337 WILD-TYPE                                                2
D42V8, multiclass
                                                  clus
vv                                                 ZNF337 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ZNF337 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, continuous
[1] "Remove cluster labels:" "ZNF337 MUTATED"        
clus
  ZNF337 MUTATED ZNF337 WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-IB-7885 
"ZNF337 WILD-TYPE" "ZNF337 WILD-TYPE" "ZNF337 WILD-TYPE" "ZNF337 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-LB-A7SX 
"ZNF337 WILD-TYPE" "ZNF337 WILD-TYPE" "ZNF337 WILD-TYPE" "ZNF337 WILD-TYPE" 
      TCGA-OE-A75W 
"ZNF337 WILD-TYPE" 
D42V10, binary
                  cls
clus                0  1
  ZNF337 MUTATED    3  1
  ZNF337 WILD-TYPE 21  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF337 MUTATED      3    1
  ZNF337 WILD-TYPE   21    8
    clus
vv   ZNF337 MUTATED ZNF337 WILD-TYPE
  R0              3               21
  R1              1                8
[1] 2 2
[1] FALSE
D42V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF337 MUTATED       1                         0     3
  ZNF337 WILD-TYPE     1                         3    25
D42V12, multiclass
                           clus
vv                          ZNF337 MUTATED ZNF337 WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = TAOK2 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2              0  1
  TAOK2 MUTATED    2  1
  TAOK2 WILD-TYPE 16  4
  TAOK2 MUTATED TAOK2 WILD-TYPE 
              3              20 
  TAOK2 MUTATED TAOK2 WILD-TYPE 
              1               4 
$`TAOK2 MUTATED`
TCGA-FB-A5VM TCGA-IB-7651 TCGA-IB-A5SO 
         449         1989          329 

$`TAOK2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  TAOK2 MUTATED TAOK2 WILD-TYPE 
            329               1 
  TAOK2 MUTATED TAOK2 WILD-TYPE 
           1989            1991 
  TAOK2 MUTATED TAOK2 WILD-TYPE 
            449             233 
[1] "329.0 - 1989.0 (449.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.3"
D43V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TAOK2 MUTATED          1         0         3         0        0
  TAOK2 WILD-TYPE        1         6        20         1        1
D43V3, multiclass
           clus
vv          TAOK2 MUTATED TAOK2 WILD-TYPE
  STAGE IB              1               1
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  TAOK2 MUTATED          4
  TAOK2 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D43V5, binary
                 cls
clus               0  1
  TAOK2 MUTATED    1  3
  TAOK2 WILD-TYPE  6 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK2 MUTATED      1    3
  TAOK2 WILD-TYPE    6   22
   clus
vv  TAOK2 MUTATED TAOK2 WILD-TYPE
  0             1               6
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  TAOK2 MUTATED    3  0  1
  TAOK2 WILD-TYPE 16  1 12
D43V6, multiclass
    clus
vv   TAOK2 MUTATED TAOK2 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                 cls
clus               0  1
  TAOK2 MUTATED    2  2
  TAOK2 WILD-TYPE 12 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK2 MUTATED      2    2
  TAOK2 WILD-TYPE   12   17
        clus
vv       TAOK2 MUTATED TAOK2 WILD-TYPE
  FEMALE             2              12
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TAOK2 MUTATED                                     4
  TAOK2 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TAOK2 MUTATED                                       0
  TAOK2 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TAOK2 MUTATED                                                  0
  TAOK2 WILD-TYPE                                                2
D43V8, multiclass
                                                  clus
vv                                                 TAOK2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 TAOK2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, continuous
[1] "Remove cluster labels:" "TAOK2 MUTATED"         
clus
  TAOK2 MUTATED TAOK2 WILD-TYPE 
              2               9 
     TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1      TCGA-IB-7885 
"TAOK2 WILD-TYPE" "TAOK2 WILD-TYPE" "TAOK2 WILD-TYPE" "TAOK2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"TAOK2 WILD-TYPE" "TAOK2 WILD-TYPE" "TAOK2 WILD-TYPE" "TAOK2 WILD-TYPE" 
     TCGA-OE-A75W 
"TAOK2 WILD-TYPE" 
D43V10, binary
                 cls
clus               0  1
  TAOK2 MUTATED    4  0
  TAOK2 WILD-TYPE 20  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK2 MUTATED      4    0
  TAOK2 WILD-TYPE   20    9
    clus
vv   TAOK2 MUTATED TAOK2 WILD-TYPE
  R0             4              20
  R1             0               9
[1] 2 2
[1] FALSE
D43V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TAOK2 MUTATED       0                         0     4
  TAOK2 WILD-TYPE     2                         3    24
D43V12, multiclass
                           clus
vv                          TAOK2 MUTATED TAOK2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = UNC5A MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2              0  1
  UNC5A MUTATED    0  2
  UNC5A WILD-TYPE 18  3
  UNC5A MUTATED UNC5A WILD-TYPE 
              2              21 
  UNC5A MUTATED UNC5A WILD-TYPE 
              2               3 
$`UNC5A MUTATED`
TCGA-F2-A44G TCGA-IB-7651 
         153         1989 

$`UNC5A WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  UNC5A MUTATED UNC5A WILD-TYPE 
            153               1 
  UNC5A MUTATED UNC5A WILD-TYPE 
           1989            1991 
  UNC5A MUTATED UNC5A WILD-TYPE 
           1071             329 
[1] "153.0 - 1989.0 (1071.0)" "1.0 - 1991.0 (329.0)"   
[1] "Remove cluster labels:" "UNC5A MUTATED"         
D44V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  UNC5A MUTATED          1         0         2         0        0
  UNC5A WILD-TYPE        1         6        21         1        1
D44V3, multiclass
           clus
vv          UNC5A MUTATED UNC5A WILD-TYPE
  STAGE IB              1               1
  STAGE IIA             0               6
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  UNC5A MUTATED          3
  UNC5A WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D44V5, binary
                 cls
clus               0  1
  UNC5A MUTATED    1  2
  UNC5A WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5A MUTATED      1    2
  UNC5A WILD-TYPE    6   23
   clus
vv  UNC5A MUTATED UNC5A WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  UNC5A MUTATED    3  0  0
  UNC5A WILD-TYPE 16  1 13
D44V6, multiclass
    clus
vv   UNC5A MUTATED UNC5A WILD-TYPE
  M0             3              16
  M1             0               1
  MX             0              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                 cls
clus               0  1
  UNC5A MUTATED    3  0
  UNC5A WILD-TYPE 11 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5A MUTATED      3    0
  UNC5A WILD-TYPE   11   19
        clus
vv       UNC5A MUTATED UNC5A WILD-TYPE
  FEMALE             3              11
  MALE               0              19
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UNC5A MUTATED                                     3
  UNC5A WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UNC5A MUTATED                                       0
  UNC5A WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UNC5A MUTATED                                                  0
  UNC5A WILD-TYPE                                                2
D44V8, multiclass
                                                  clus
vv                                                 UNC5A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 UNC5A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, continuous
[1] "Remove cluster labels:" "UNC5A MUTATED"         
clus
  UNC5A MUTATED UNC5A WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"UNC5A WILD-TYPE" "UNC5A WILD-TYPE" "UNC5A WILD-TYPE" "UNC5A WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"UNC5A WILD-TYPE" "UNC5A WILD-TYPE" "UNC5A WILD-TYPE" "UNC5A WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"UNC5A WILD-TYPE" "UNC5A WILD-TYPE" 
D44V10, binary
                 cls
clus               0  1
  UNC5A MUTATED    2  1
  UNC5A WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5A MUTATED      2    1
  UNC5A WILD-TYPE   22    8
    clus
vv   UNC5A MUTATED UNC5A WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D44V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UNC5A MUTATED       0                         0     3
  UNC5A WILD-TYPE     2                         3    25
D44V12, multiclass
                           clus
vv                          UNC5A MUTATED UNC5A WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = TNFSF9 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2               0  1
  TNFSF9 MUTATED    2  2
  TNFSF9 WILD-TYPE 16  3
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
               4               19 
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
               2                3 
$`TNFSF9 MUTATED`
TCGA-F2-7273 TCGA-HZ-7925 TCGA-IB-7651 TCGA-LB-A7SX 
         360          361         1989          127 

$`TNFSF9 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
          11           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W TCGA-Q3-A5QY 
         300         1991            8         1968          110          416 
TCGA-US-A776 
         844 

  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
             127                1 
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
            1989             1991 
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
           360.5            300.0 
[1] "127.0 - 1989.0 (360.5)" "1.0 - 1991.0 (300.0)"  
[1] "hr=" "2.2"
D45V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TNFSF9 MUTATED          0         0         4         0        0
  TNFSF9 WILD-TYPE        2         6        19         1        1
D45V3, multiclass
           clus
vv          TNFSF9 MUTATED TNFSF9 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              0                6
  STAGE IIB              4               19
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  TNFSF9 MUTATED          4
  TNFSF9 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D45V5, binary
                  cls
clus                0  1
  TNFSF9 MUTATED    0  4
  TNFSF9 WILD-TYPE  7 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNFSF9 MUTATED      0    4
  TNFSF9 WILD-TYPE    7   21
   clus
vv  TNFSF9 MUTATED TNFSF9 WILD-TYPE
  0              0                7
  1              4               21
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  TNFSF9 MUTATED    2  0  2
  TNFSF9 WILD-TYPE 17  1 11
D45V6, multiclass
    clus
vv   TNFSF9 MUTATED TNFSF9 WILD-TYPE
  M0              2               17
  M1              0                1
  MX              2               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                  cls
clus                0  1
  TNFSF9 MUTATED    2  2
  TNFSF9 WILD-TYPE 12 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNFSF9 MUTATED      2    2
  TNFSF9 WILD-TYPE   12   17
        clus
vv       TNFSF9 MUTATED TNFSF9 WILD-TYPE
  FEMALE              2               12
  MALE                2               17
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TNFSF9 MUTATED                                     4
  TNFSF9 WILD-TYPE                                  24
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TNFSF9 MUTATED                                       0
  TNFSF9 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TNFSF9 MUTATED                                                  0
  TNFSF9 WILD-TYPE                                                2
D45V8, multiclass
                                                  clus
vv                                                 TNFSF9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 TNFSF9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, continuous
[1] "Remove cluster labels:" "TNFSF9 MUTATED"        
clus
  TNFSF9 MUTATED TNFSF9 WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-H8-A6C1 
"TNFSF9 WILD-TYPE" "TNFSF9 WILD-TYPE" "TNFSF9 WILD-TYPE" "TNFSF9 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A5SS       TCGA-IB-A6UG 
"TNFSF9 WILD-TYPE" "TNFSF9 WILD-TYPE" "TNFSF9 WILD-TYPE" "TNFSF9 WILD-TYPE" 
      TCGA-OE-A75W 
"TNFSF9 WILD-TYPE" 
D45V10, binary
                  cls
clus                0  1
  TNFSF9 MUTATED    2  2
  TNFSF9 WILD-TYPE 22  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNFSF9 MUTATED      2    2
  TNFSF9 WILD-TYPE   22    7
    clus
vv   TNFSF9 MUTATED TNFSF9 WILD-TYPE
  R0              2               22
  R1              2                7
[1] 2 2
[1] FALSE
D45V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNFSF9 MUTATED       0                         2     2
  TNFSF9 WILD-TYPE     2                         1    26
D45V12, multiclass
                           clus
vv                          TNFSF9 MUTATED TNFSF9 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              2                1
  WHITE                                  2               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = TEX2 MUTATION ANALYSIS
D46V1, survival
                sevent
clus2             0  1
  TEX2 MUTATED    1  2
  TEX2 WILD-TYPE 17  3
  TEX2 MUTATED TEX2 WILD-TYPE 
             3             20 
  TEX2 MUTATED TEX2 WILD-TYPE 
             2              3 
$`TEX2 MUTATED`
TCGA-F2-A44G TCGA-IB-7651 TCGA-IB-8126 
         153         1989           17 

$`TEX2 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
         361           11           13          476          851          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  TEX2 MUTATED TEX2 WILD-TYPE 
            17              1 
  TEX2 MUTATED TEX2 WILD-TYPE 
          1989           1991 
  TEX2 MUTATED TEX2 WILD-TYPE 
         153.0          344.5 
[1] "17.0 - 1989.0 (153.0)" "1.0 - 1991.0 (344.5)" 
[1] "hr=" "3.4"
D46V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TEX2 MUTATED          0         0         3         1        0
  TEX2 WILD-TYPE        2         6        20         0        1
D46V3, multiclass
           clus
vv          TEX2 MUTATED TEX2 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            3             20
  STAGE III            1              0
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  TEX2 MUTATED          4
  TEX2 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D46V5, binary
                cls
clus              0  1
  TEX2 MUTATED    0  4
  TEX2 WILD-TYPE  7 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      0    4
  TEX2 WILD-TYPE    7   21
   clus
vv  TEX2 MUTATED TEX2 WILD-TYPE
  0            0              7
  1            4             21
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  TEX2 MUTATED    3  0  1
  TEX2 WILD-TYPE 16  1 12
D46V6, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  M0            3             16
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                cls
clus              0  1
  TEX2 MUTATED    4  0
  TEX2 WILD-TYPE 10 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      4    0
  TEX2 WILD-TYPE   10   19
        clus
vv       TEX2 MUTATED TEX2 WILD-TYPE
  FEMALE            4             10
  MALE              0             19
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TEX2 MUTATED                                     4
  TEX2 WILD-TYPE                                  24
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TEX2 MUTATED                                       0
  TEX2 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TEX2 MUTATED                                                  0
  TEX2 WILD-TYPE                                                2
D46V8, multiclass
                                                  clus
vv                                                 TEX2 MUTATED TEX2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4             24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D46V9, continuous
[1] "Remove cluster labels:" "TEX2 MUTATED"          
clus
  TEX2 MUTATED TEX2 WILD-TYPE 
             2              9 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-A5SS     TCGA-IB-A6UG     TCGA-LB-A7SX 
"TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" "TEX2 WILD-TYPE" 
    TCGA-OE-A75W 
"TEX2 WILD-TYPE" 
D46V10, binary
                cls
clus              0  1
  TEX2 MUTATED    2  2
  TEX2 WILD-TYPE 22  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      2    2
  TEX2 WILD-TYPE   22    7
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  R0            2             22
  R1            2              7
[1] 2 2
[1] FALSE
D46V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TEX2 MUTATED       0                         0     4
  TEX2 WILD-TYPE     2                         3    24
D46V12, multiclass
                           clus
vv                          TEX2 MUTATED TEX2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                4             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = RBM43 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2              0  1
  RBM43 MUTATED    1  0
  RBM43 WILD-TYPE 17  5
  RBM43 MUTATED RBM43 WILD-TYPE 
              1              22 
  RBM43 MUTATED RBM43 WILD-TYPE 
              0               5 
$`RBM43 MUTATED`
TCGA-FB-A78T 
           1 

$`RBM43 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
         361           11           13         1989          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         127          110          416          844 

  RBM43 MUTATED RBM43 WILD-TYPE 
              1               8 
  RBM43 MUTATED RBM43 WILD-TYPE 
              1            1991 
  RBM43 MUTATED RBM43 WILD-TYPE 
            1.0           344.5 
[1] "1.0 - 1.0 (1.0)"      "8.0 - 1991.0 (344.5)"
[1] "Remove cluster labels:" "RBM43 MUTATED"         
D47V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RBM43 MUTATED          0         1         2         0        0
  RBM43 WILD-TYPE        2         5        21         1        1
D47V3, multiclass
           clus
vv          RBM43 MUTATED RBM43 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  RBM43 MUTATED          3
  RBM43 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D47V5, binary
                 cls
clus               0  1
  RBM43 MUTATED    1  2
  RBM43 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM43 MUTATED      1    2
  RBM43 WILD-TYPE    6   23
   clus
vv  RBM43 MUTATED RBM43 WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  RBM43 MUTATED    2  0  1
  RBM43 WILD-TYPE 17  1 12
D47V6, multiclass
    clus
vv   RBM43 MUTATED RBM43 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                 cls
clus               0  1
  RBM43 MUTATED    1  2
  RBM43 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM43 MUTATED      1    2
  RBM43 WILD-TYPE   13   17
        clus
vv       RBM43 MUTATED RBM43 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM43 MUTATED                                     3
  RBM43 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM43 MUTATED                                       0
  RBM43 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM43 MUTATED                                                  0
  RBM43 WILD-TYPE                                                2
D47V8, multiclass
                                                  clus
vv                                                 RBM43 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RBM43 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, continuous
[1] "Remove cluster labels:" "RBM43 MUTATED"         
clus
  RBM43 MUTATED RBM43 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A7DR      TCGA-H8-A6C1      TCGA-IB-7651 
"RBM43 WILD-TYPE" "RBM43 WILD-TYPE" "RBM43 WILD-TYPE" "RBM43 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"RBM43 WILD-TYPE" "RBM43 WILD-TYPE" "RBM43 WILD-TYPE" "RBM43 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"RBM43 WILD-TYPE" "RBM43 WILD-TYPE" 
D47V10, binary
                 cls
clus               0  1
  RBM43 MUTATED    2  1
  RBM43 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM43 MUTATED      2    1
  RBM43 WILD-TYPE   22    8
    clus
vv   RBM43 MUTATED RBM43 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D47V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM43 MUTATED       0                         0     3
  RBM43 WILD-TYPE     2                         3    25
D47V12, multiclass
                           clus
vv                          RBM43 MUTATED RBM43 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = CIR1 MUTATION ANALYSIS
D48V1, survival
                sevent
clus2             0  1
  CIR1 MUTATED    1  2
  CIR1 WILD-TYPE 17  3
  CIR1 MUTATED CIR1 WILD-TYPE 
             3             20 
  CIR1 MUTATED CIR1 WILD-TYPE 
             2              3 
$`CIR1 MUTATED`
TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A6UG 
          13         1989         1968 

$`CIR1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28          361           11          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-LB-A7SX TCGA-OE-A75W 
         329          300         1991            8          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  CIR1 MUTATED CIR1 WILD-TYPE 
            13              1 
  CIR1 MUTATED CIR1 WILD-TYPE 
          1989           1991 
  CIR1 MUTATED CIR1 WILD-TYPE 
        1968.0          314.5 
[1] "13.0 - 1989.0 (1968.0)" "1.0 - 1991.0 (314.5)"  
[1] "hr=" "2"  
D48V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CIR1 MUTATED          0         0         3         0        0
  CIR1 WILD-TYPE        2         6        20         1        1
D48V3, multiclass
           clus
vv          CIR1 MUTATED CIR1 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            3             20
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  CIR1 MUTATED          3
  CIR1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D48V5, binary
                cls
clus              0  1
  CIR1 MUTATED    0  3
  CIR1 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      0    3
  CIR1 WILD-TYPE    7   22
   clus
vv  CIR1 MUTATED CIR1 WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  CIR1 MUTATED    2  0  1
  CIR1 WILD-TYPE 17  1 12
D48V6, multiclass
    clus
vv   CIR1 MUTATED CIR1 WILD-TYPE
  M0            2             17
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                cls
clus              0  1
  CIR1 MUTATED    1  2
  CIR1 WILD-TYPE 13 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      1    2
  CIR1 WILD-TYPE   13   17
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  FEMALE            1             13
  MALE              2             17
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CIR1 MUTATED                                     2
  CIR1 WILD-TYPE                                  26
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CIR1 MUTATED                                       1
  CIR1 WILD-TYPE                                     2
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CIR1 MUTATED                                                  0
  CIR1 WILD-TYPE                                                2
D48V8, multiclass
                                                  clus
vv                                                 CIR1 MUTATED CIR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2             26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1              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"
D48V9, continuous
[1] "Remove cluster labels:" "CIR1 MUTATED"          
clus
  CIR1 MUTATED CIR1 WILD-TYPE 
             2              9 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-LB-A7SX 
"CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" "CIR1 WILD-TYPE" 
    TCGA-OE-A75W 
"CIR1 WILD-TYPE" 
D48V10, binary
                cls
clus              0  1
  CIR1 MUTATED    2  1
  CIR1 WILD-TYPE 22  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      2    1
  CIR1 WILD-TYPE   22    8
    clus
vv   CIR1 MUTATED CIR1 WILD-TYPE
  R0            2             22
  R1            1              8
[1] 2 2
[1] FALSE
D48V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CIR1 MUTATED       0                         0     3
  CIR1 WILD-TYPE     2                         3    25
D48V12, multiclass
                           clus
vv                          CIR1 MUTATED CIR1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = TOX4 MUTATION ANALYSIS
D49V1, survival
                sevent
clus2             0  1
  TOX4 MUTATED    0  3
  TOX4 WILD-TYPE 18  2
  TOX4 MUTATED TOX4 WILD-TYPE 
             3             20 
  TOX4 MUTATED TOX4 WILD-TYPE 
             3              2 
$`TOX4 MUTATED`
TCGA-IB-7651 TCGA-IB-A5SS TCGA-IB-A6UG 
        1989         1991         1968 

$`TOX4 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-LB-A7SX TCGA-OE-A75W 
          17          329          300            8          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  TOX4 MUTATED TOX4 WILD-TYPE 
          1968              1 
  TOX4 MUTATED TOX4 WILD-TYPE 
          1991            851 
  TOX4 MUTATED TOX4 WILD-TYPE 
          1989            233 
[1] "1968.0 - 1991.0 (1989.0)" "1.0 - 851.0 (233.0)"     
[1] "hr="     "2.8e+08"
D49V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TOX4 MUTATED          1         0         3         0        0
  TOX4 WILD-TYPE        1         6        20         1        1
D49V3, multiclass
           clus
vv          TOX4 MUTATED TOX4 WILD-TYPE
  STAGE IB             1              1
  STAGE IIA            0              6
  STAGE IIB            3             20
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  TOX4 MUTATED          4
  TOX4 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D49V5, binary
                cls
clus              0  1
  TOX4 MUTATED    1  3
  TOX4 WILD-TYPE  6 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOX4 MUTATED      1    3
  TOX4 WILD-TYPE    6   22
   clus
vv  TOX4 MUTATED TOX4 WILD-TYPE
  0            1              6
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  TOX4 MUTATED    4  0  0
  TOX4 WILD-TYPE 15  1 13
D49V6, multiclass
    clus
vv   TOX4 MUTATED TOX4 WILD-TYPE
  M0            4             15
  M1            0              1
  MX            0             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                cls
clus              0  1
  TOX4 MUTATED    3  1
  TOX4 WILD-TYPE 11 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOX4 MUTATED      3    1
  TOX4 WILD-TYPE   11   18
        clus
vv       TOX4 MUTATED TOX4 WILD-TYPE
  FEMALE            3             11
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TOX4 MUTATED                                     4
  TOX4 WILD-TYPE                                  24
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TOX4 MUTATED                                       0
  TOX4 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TOX4 MUTATED                                                  0
  TOX4 WILD-TYPE                                                2
D49V8, multiclass
                                                  clus
vv                                                 TOX4 MUTATED TOX4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4             24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D49V9, continuous
D49V10, binary
                cls
clus              0  1
  TOX4 MUTATED    3  1
  TOX4 WILD-TYPE 21  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOX4 MUTATED      3    1
  TOX4 WILD-TYPE   21    8
    clus
vv   TOX4 MUTATED TOX4 WILD-TYPE
  R0            3             21
  R1            1              8
[1] 2 2
[1] FALSE
D49V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TOX4 MUTATED       0                         0     4
  TOX4 WILD-TYPE     2                         3    24
D49V12, multiclass
                           clus
vv                          TOX4 MUTATED TOX4 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                4             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = HIBCH MUTATION ANALYSIS
D50V1, survival
                 sevent
clus2              0  1
  HIBCH MUTATED    2  0
  HIBCH WILD-TYPE 16  5
  HIBCH MUTATED HIBCH WILD-TYPE 
              2              21 
  HIBCH MUTATED HIBCH WILD-TYPE 
              0               5 
$`HIBCH MUTATED`
TCGA-HZ-7918 TCGA-HZ-7925 
          28          361 

$`HIBCH WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          11           13         1989          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  HIBCH MUTATED HIBCH WILD-TYPE 
             28               1 
  HIBCH MUTATED HIBCH WILD-TYPE 
            361            1991 
  HIBCH MUTATED HIBCH WILD-TYPE 
          194.5           329.0 
[1] "28.0 - 361.0 (194.5)" "1.0 - 1991.0 (329.0)"
[1] "Remove cluster labels:" "HIBCH MUTATED"         
D50V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  HIBCH MUTATED          0         0         3         0        0
  HIBCH WILD-TYPE        2         6        20         1        1
D50V3, multiclass
           clus
vv          HIBCH MUTATED HIBCH WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  HIBCH MUTATED          3
  HIBCH WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D50V5, binary
                 cls
clus               0  1
  HIBCH MUTATED    0  3
  HIBCH WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIBCH MUTATED      0    3
  HIBCH WILD-TYPE    7   22
   clus
vv  HIBCH MUTATED HIBCH WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  HIBCH MUTATED    1  0  2
  HIBCH WILD-TYPE 18  1 11
D50V6, multiclass
    clus
vv   HIBCH MUTATED HIBCH WILD-TYPE
  M0             1              18
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                 cls
clus               0  1
  HIBCH MUTATED    1  2
  HIBCH WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIBCH MUTATED      1    2
  HIBCH WILD-TYPE   13   17
        clus
vv       HIBCH MUTATED HIBCH WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIBCH MUTATED                                     3
  HIBCH WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIBCH MUTATED                                       0
  HIBCH WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIBCH MUTATED                                                  0
  HIBCH WILD-TYPE                                                2
D50V8, multiclass
                                                  clus
vv                                                 HIBCH MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 HIBCH WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, continuous
D50V10, binary
                 cls
clus               0  1
  HIBCH MUTATED    3  0
  HIBCH WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIBCH MUTATED      3    0
  HIBCH WILD-TYPE   21    9
    clus
vv   HIBCH MUTATED HIBCH WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D50V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIBCH MUTATED       0                         0     3
  HIBCH WILD-TYPE     2                         3    25
D50V12, multiclass
                           clus
vv                          HIBCH MUTATED HIBCH WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = CRAT MUTATION ANALYSIS
D51V1, survival
                sevent
clus2             0  1
  CRAT MUTATED    2  0
  CRAT WILD-TYPE 16  5
  CRAT MUTATED CRAT WILD-TYPE 
             2             21 
  CRAT MUTATED CRAT WILD-TYPE 
             0              5 
$`CRAT MUTATED`
TCGA-IB-8126 TCGA-IB-A5SO 
          17          329 

$`CRAT WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 
          28          361           11           13         1989          476 
TCGA-IB-7885 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         851          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  CRAT MUTATED CRAT WILD-TYPE 
            17              1 
  CRAT MUTATED CRAT WILD-TYPE 
           329           1991 
  CRAT MUTATED CRAT WILD-TYPE 
           173            360 
[1] "17.0 - 329.0 (173.0)" "1.0 - 1991.0 (360.0)"
[1] "Remove cluster labels:" "CRAT MUTATED"          
D51V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CRAT MUTATED          0         0         2         1        0
  CRAT WILD-TYPE        2         6        21         0        1
D51V3, multiclass
           clus
vv          CRAT MUTATED CRAT WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            2             21
  STAGE III            1              0
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  CRAT MUTATED          3
  CRAT WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D51V5, binary
                cls
clus              0  1
  CRAT MUTATED    0  3
  CRAT WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED      0    3
  CRAT WILD-TYPE    7   22
   clus
vv  CRAT MUTATED CRAT WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  CRAT MUTATED    2  0  1
  CRAT WILD-TYPE 17  1 12
D51V6, multiclass
    clus
vv   CRAT MUTATED CRAT WILD-TYPE
  M0            2             17
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                cls
clus              0  1
  CRAT MUTATED    2  1
  CRAT WILD-TYPE 12 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED      2    1
  CRAT WILD-TYPE   12   18
        clus
vv       CRAT MUTATED CRAT WILD-TYPE
  FEMALE            2             12
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CRAT MUTATED                                     3
  CRAT WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CRAT MUTATED                                       0
  CRAT WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CRAT MUTATED                                                  0
  CRAT WILD-TYPE                                                2
D51V8, multiclass
                                                  clus
vv                                                 CRAT MUTATED CRAT WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D51V9, continuous
[1] "Remove cluster labels:" "CRAT MUTATED"          
clus
  CRAT MUTATED CRAT WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-A5SS     TCGA-IB-A6UG 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" "CRAT WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"CRAT WILD-TYPE" "CRAT WILD-TYPE" 
D51V10, binary
                cls
clus              0  1
  CRAT MUTATED    2  1
  CRAT WILD-TYPE 22  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRAT MUTATED      2    1
  CRAT WILD-TYPE   22    8
    clus
vv   CRAT MUTATED CRAT WILD-TYPE
  R0            2             22
  R1            1              8
[1] 2 2
[1] FALSE
D51V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CRAT MUTATED       0                         0     3
  CRAT WILD-TYPE     2                         3    25
D51V12, multiclass
                           clus
vv                          CRAT MUTATED CRAT WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = SRP14 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2              0  1
  SRP14 MUTATED    2  1
  SRP14 WILD-TYPE 16  4
  SRP14 MUTATED SRP14 WILD-TYPE 
              3              20 
  SRP14 MUTATED SRP14 WILD-TYPE 
              1               4 
$`SRP14 MUTATED`
TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-A6UG 
         361           13         1968 

$`SRP14 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28           11         1989          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-LB-A7SX TCGA-OE-A75W 
         329          300         1991            8          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  SRP14 MUTATED SRP14 WILD-TYPE 
             13               1 
  SRP14 MUTATED SRP14 WILD-TYPE 
           1968            1991 
  SRP14 MUTATED SRP14 WILD-TYPE 
          361.0           314.5 
[1] "13.0 - 1968.0 (361.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.9"
D52V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SRP14 MUTATED          0         0         3         0        0
  SRP14 WILD-TYPE        2         6        20         1        1
D52V3, multiclass
           clus
vv          SRP14 MUTATED SRP14 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  SRP14 MUTATED          3
  SRP14 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D52V5, binary
                 cls
clus               0  1
  SRP14 MUTATED    0  3
  SRP14 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      0    3
  SRP14 WILD-TYPE    7   22
   clus
vv  SRP14 MUTATED SRP14 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  SRP14 MUTATED    1  0  2
  SRP14 WILD-TYPE 18  1 11
D52V6, multiclass
    clus
vv   SRP14 MUTATED SRP14 WILD-TYPE
  M0             1              18
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                 cls
clus               0  1
  SRP14 MUTATED    0  3
  SRP14 WILD-TYPE 14 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      0    3
  SRP14 WILD-TYPE   14   16
        clus
vv       SRP14 MUTATED SRP14 WILD-TYPE
  FEMALE             0              14
  MALE               3              16
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SRP14 MUTATED                                     2
  SRP14 WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SRP14 MUTATED                                       1
  SRP14 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SRP14 MUTATED                                                  0
  SRP14 WILD-TYPE                                                2
D52V8, multiclass
                                                  clus
vv                                                 SRP14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SRP14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, continuous
[1] "Remove cluster labels:" "SRP14 MUTATED"         
clus
  SRP14 MUTATED SRP14 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"SRP14 WILD-TYPE" "SRP14 WILD-TYPE" 
D52V10, binary
                 cls
clus               0  1
  SRP14 MUTATED    2  1
  SRP14 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRP14 MUTATED      2    1
  SRP14 WILD-TYPE   22    8
    clus
vv   SRP14 MUTATED SRP14 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D52V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SRP14 MUTATED       0                         0     3
  SRP14 WILD-TYPE     2                         3    25
D52V12, multiclass
                           clus
vv                          SRP14 MUTATED SRP14 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = PDZD7 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2              0  1
  PDZD7 MUTATED    2  1
  PDZD7 WILD-TYPE 16  4
  PDZD7 MUTATED PDZD7 WILD-TYPE 
              3              20 
  PDZD7 MUTATED PDZD7 WILD-TYPE 
              1               4 
$`PDZD7 MUTATED`
TCGA-IB-7651 TCGA-IB-8126 TCGA-Q3-A5QY 
        1989           17          416 

$`PDZD7 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-US-A776 
         110          844 

  PDZD7 MUTATED PDZD7 WILD-TYPE 
             17               1 
  PDZD7 MUTATED PDZD7 WILD-TYPE 
           1989            1991 
  PDZD7 MUTATED PDZD7 WILD-TYPE 
          416.0           314.5 
[1] "17.0 - 1989.0 (416.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.2"
D53V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PDZD7 MUTATED          0         0         2         1        0
  PDZD7 WILD-TYPE        2         6        21         0        1
D53V3, multiclass
           clus
vv          PDZD7 MUTATED PDZD7 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             2              21
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  PDZD7 MUTATED          3
  PDZD7 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D53V5, binary
                 cls
clus               0  1
  PDZD7 MUTATED    0  3
  PDZD7 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD7 MUTATED      0    3
  PDZD7 WILD-TYPE    7   22
   clus
vv  PDZD7 MUTATED PDZD7 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  PDZD7 MUTATED    2  0  1
  PDZD7 WILD-TYPE 17  1 12
D53V6, multiclass
    clus
vv   PDZD7 MUTATED PDZD7 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                 cls
clus               0  1
  PDZD7 MUTATED    2  1
  PDZD7 WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD7 MUTATED      2    1
  PDZD7 WILD-TYPE   12   18
        clus
vv       PDZD7 MUTATED PDZD7 WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDZD7 MUTATED                                     3
  PDZD7 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDZD7 MUTATED                                       0
  PDZD7 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDZD7 MUTATED                                                  0
  PDZD7 WILD-TYPE                                                2
D53V8, multiclass
                                                  clus
vv                                                 PDZD7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PDZD7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, continuous
[1] "Remove cluster labels:" "PDZD7 MUTATED"         
clus
  PDZD7 MUTATED PDZD7 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"PDZD7 WILD-TYPE" "PDZD7 WILD-TYPE" "PDZD7 WILD-TYPE" "PDZD7 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"PDZD7 WILD-TYPE" "PDZD7 WILD-TYPE" "PDZD7 WILD-TYPE" "PDZD7 WILD-TYPE" 
     TCGA-OE-A75W 
"PDZD7 WILD-TYPE" 
D53V10, binary
                 cls
clus               0  1
  PDZD7 MUTATED    2  1
  PDZD7 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD7 MUTATED      2    1
  PDZD7 WILD-TYPE   22    8
    clus
vv   PDZD7 MUTATED PDZD7 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D53V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDZD7 MUTATED       0                         0     3
  PDZD7 WILD-TYPE     2                         3    25
D53V12, multiclass
                           clus
vv                          PDZD7 MUTATED PDZD7 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = POP5 MUTATION ANALYSIS
D54V1, survival
                sevent
clus2             0  1
  POP5 MUTATED    3  0
  POP5 WILD-TYPE 15  5
  POP5 MUTATED POP5 WILD-TYPE 
             3             20 
  POP5 MUTATED POP5 WILD-TYPE 
             0              5 
$`POP5 MUTATED`
TCGA-IB-8126 TCGA-IB-A5SP TCGA-US-A776 
          17          300          844 

$`POP5 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 
          28          361           11           13         1989          476 
TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         851          329         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY 
         110          416 

  POP5 MUTATED POP5 WILD-TYPE 
            17              1 
  POP5 MUTATED POP5 WILD-TYPE 
           844           1991 
  POP5 MUTATED POP5 WILD-TYPE 
         300.0          344.5 
[1] "17.0 - 844.0 (300.0)" "1.0 - 1991.0 (344.5)"
[1] "hr="   "8e+07"
D54V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  POP5 MUTATED          0         2         0         1        0
  POP5 WILD-TYPE        2         4        23         0        1
D54V3, multiclass
           clus
vv          POP5 MUTATED POP5 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            2              4
  STAGE IIB            0             23
  STAGE III            1              0
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  POP5 MUTATED          3
  POP5 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D54V5, binary
                cls
clus              0  1
  POP5 MUTATED    2  1
  POP5 WILD-TYPE  5 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP5 MUTATED      2    1
  POP5 WILD-TYPE    5   24
   clus
vv  POP5 MUTATED POP5 WILD-TYPE
  0            2              5
  1            1             24
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  POP5 MUTATED    2  0  1
  POP5 WILD-TYPE 17  1 12
D54V6, multiclass
    clus
vv   POP5 MUTATED POP5 WILD-TYPE
  M0            2             17
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                cls
clus              0  1
  POP5 MUTATED    1  2
  POP5 WILD-TYPE 13 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP5 MUTATED      1    2
  POP5 WILD-TYPE   13   17
        clus
vv       POP5 MUTATED POP5 WILD-TYPE
  FEMALE            1             13
  MALE              2             17
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  POP5 MUTATED                                     2
  POP5 WILD-TYPE                                  26
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  POP5 MUTATED                                       0
  POP5 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  POP5 MUTATED                                                  1
  POP5 WILD-TYPE                                                1
D54V8, multiclass
                                                  clus
vv                                                 POP5 MUTATED POP5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         2             26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              3
  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"
D54V9, continuous
[1] "Remove cluster labels:" "POP5 MUTATED"          
clus
  POP5 MUTATED POP5 WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-IB-7651     TCGA-IB-7885     TCGA-IB-A5SS     TCGA-IB-A6UG 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" "POP5 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"POP5 WILD-TYPE" "POP5 WILD-TYPE" 
D54V10, binary
                cls
clus              0  1
  POP5 MUTATED    1  2
  POP5 WILD-TYPE 23  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  POP5 MUTATED      1    2
  POP5 WILD-TYPE   23    7
    clus
vv   POP5 MUTATED POP5 WILD-TYPE
  R0            1             23
  R1            2              7
[1] 2 2
[1] FALSE
D54V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POP5 MUTATED       0                         0     3
  POP5 WILD-TYPE     2                         3    25
D54V12, multiclass
                           clus
vv                          POP5 MUTATED POP5 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = UNC5D MUTATION ANALYSIS
D55V1, survival
                 sevent
clus2              0  1
  UNC5D MUTATED    2  1
  UNC5D WILD-TYPE 16  4
  UNC5D MUTATED UNC5D WILD-TYPE 
              3              20 
  UNC5D MUTATED UNC5D WILD-TYPE 
              1               4 
$`UNC5D MUTATED`
TCGA-IB-7651 TCGA-IB-8126 TCGA-LB-A7SX 
        1989           17          127 

$`UNC5D WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W 
         329          300         1991            8         1968          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  UNC5D MUTATED UNC5D WILD-TYPE 
             17               1 
  UNC5D MUTATED UNC5D WILD-TYPE 
           1989            1991 
  UNC5D MUTATED UNC5D WILD-TYPE 
          127.0           344.5 
[1] "17.0 - 1989.0 (127.0)" "1.0 - 1991.0 (344.5)" 
[1] "hr=" "1"  
D55V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  UNC5D MUTATED          0         0         2         1        0
  UNC5D WILD-TYPE        2         6        21         0        1
D55V3, multiclass
           clus
vv          UNC5D MUTATED UNC5D WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             2              21
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  UNC5D MUTATED          3
  UNC5D WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D55V5, binary
                 cls
clus               0  1
  UNC5D MUTATED    0  3
  UNC5D WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5D MUTATED      0    3
  UNC5D WILD-TYPE    7   22
   clus
vv  UNC5D MUTATED UNC5D WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  UNC5D MUTATED    2  0  1
  UNC5D WILD-TYPE 17  1 12
D55V6, multiclass
    clus
vv   UNC5D MUTATED UNC5D WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                 cls
clus               0  1
  UNC5D MUTATED    3  0
  UNC5D WILD-TYPE 11 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5D MUTATED      3    0
  UNC5D WILD-TYPE   11   19
        clus
vv       UNC5D MUTATED UNC5D WILD-TYPE
  FEMALE             3              11
  MALE               0              19
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UNC5D MUTATED                                     3
  UNC5D WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UNC5D MUTATED                                       0
  UNC5D WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UNC5D MUTATED                                                  0
  UNC5D WILD-TYPE                                                2
D55V8, multiclass
                                                  clus
vv                                                 UNC5D MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 UNC5D WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, continuous
D55V10, binary
                 cls
clus               0  1
  UNC5D MUTATED    1  2
  UNC5D WILD-TYPE 23  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UNC5D MUTATED      1    2
  UNC5D WILD-TYPE   23    7
    clus
vv   UNC5D MUTATED UNC5D WILD-TYPE
  R0             1              23
  R1             2               7
[1] 2 2
[1] FALSE
D55V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UNC5D MUTATED       0                         1     2
  UNC5D WILD-TYPE     2                         2    26
D55V12, multiclass
                           clus
vv                          UNC5D MUTATED UNC5D WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 2              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = FAM47C MUTATION ANALYSIS
D56V1, survival
                  sevent
clus2               0  1
  FAM47C MUTATED    4  0
  FAM47C WILD-TYPE 14  5
  FAM47C MUTATED FAM47C WILD-TYPE 
               4               19 
  FAM47C MUTATED FAM47C WILD-TYPE 
               0                5 
$`FAM47C MUTATED`
TCGA-FB-A78T TCGA-IB-8126 TCGA-LB-A7SX TCGA-Q3-A5QY 
           1           17          127          416 

$`FAM47C WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
         361           11           13         1989          476          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W 
         329          300         1991            8         1968          110 
TCGA-US-A776 
         844 

  FAM47C MUTATED FAM47C WILD-TYPE 
               1                8 
  FAM47C MUTATED FAM47C WILD-TYPE 
             416             1991 
  FAM47C MUTATED FAM47C WILD-TYPE 
              72              360 
[1] "1.0 - 416.0 (72.0)"   "8.0 - 1991.0 (360.0)"
[1] "hr="     "7.5e+07"
D56V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FAM47C MUTATED          1         0         3         1        0
  FAM47C WILD-TYPE        1         6        20         0        1
D56V3, multiclass
           clus
vv          FAM47C MUTATED FAM47C WILD-TYPE
  STAGE IB               1                1
  STAGE IIA              0                6
  STAGE IIB              3               20
  STAGE III              1                0
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  FAM47C MUTATED          5
  FAM47C WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D56V5, binary
                  cls
clus                0  1
  FAM47C MUTATED    1  4
  FAM47C WILD-TYPE  6 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      1    4
  FAM47C WILD-TYPE    6   21
   clus
vv  FAM47C MUTATED FAM47C WILD-TYPE
  0              1                6
  1              4               21
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  FAM47C MUTATED    3  0  2
  FAM47C WILD-TYPE 16  1 11
D56V6, multiclass
    clus
vv   FAM47C MUTATED FAM47C WILD-TYPE
  M0              3               16
  M1              0                1
  MX              2               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                  cls
clus                0  1
  FAM47C MUTATED    4  1
  FAM47C WILD-TYPE 10 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      4    1
  FAM47C WILD-TYPE   10   18
        clus
vv       FAM47C MUTATED FAM47C WILD-TYPE
  FEMALE              4               10
  MALE                1               18
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM47C MUTATED                                     5
  FAM47C WILD-TYPE                                  23
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM47C MUTATED                                       0
  FAM47C WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM47C MUTATED                                                  0
  FAM47C WILD-TYPE                                                2
D56V8, multiclass
                                                  clus
vv                                                 FAM47C MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 FAM47C WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, continuous
D56V10, binary
                  cls
clus                0  1
  FAM47C MUTATED    3  2
  FAM47C WILD-TYPE 21  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      3    2
  FAM47C WILD-TYPE   21    7
    clus
vv   FAM47C MUTATED FAM47C WILD-TYPE
  R0              3               21
  R1              2                7
[1] 2 2
[1] FALSE
D56V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM47C MUTATED       0                         1     4
  FAM47C WILD-TYPE     2                         2    24
D56V12, multiclass
                           clus
vv                          FAM47C MUTATED FAM47C WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              1                2
  WHITE                                  4               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = TMEM184A MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  TMEM184A MUTATED    2  1
  TMEM184A WILD-TYPE 16  4
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 3                 20 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 1                  4 
$`TMEM184A MUTATED`
TCGA-FB-A5VM TCGA-HZ-A77O TCGA-IB-7651 
         449           11         1989 

$`TMEM184A WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
         361           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  TMEM184A MUTATED TMEM184A WILD-TYPE 
                11                  1 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
              1989               1991 
  TMEM184A MUTATED TMEM184A WILD-TYPE 
             449.0              314.5 
[1] "11.0 - 1989.0 (449.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.2"
D57V2, continuous
                    vv
clus                 STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TMEM184A MUTATED          2         0         2         0        0
  TMEM184A WILD-TYPE        0         6        21         1        1
D57V3, multiclass
           clus
vv          TMEM184A MUTATED TMEM184A WILD-TYPE
  STAGE IB                 2                  0
  STAGE IIA                0                  6
  STAGE IIB                2                 21
  STAGE III                0                  1
  STAGE IV                 0                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T2+T3+T4
  TMEM184A MUTATED          4
  TMEM184A WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D57V5, binary
                    cls
clus                  0  1
  TMEM184A MUTATED    2  2
  TMEM184A WILD-TYPE  5 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      2    2
  TMEM184A WILD-TYPE    5   23
   clus
vv  TMEM184A MUTATED TMEM184A WILD-TYPE
  0                2                  5
  1                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  TMEM184A MUTATED    3  0  1
  TMEM184A WILD-TYPE 16  1 12
D57V6, multiclass
    clus
vv   TMEM184A MUTATED TMEM184A WILD-TYPE
  M0                3                 16
  M1                0                  1
  MX                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                    cls
clus                  0  1
  TMEM184A MUTATED    3  1
  TMEM184A WILD-TYPE 11 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      3    1
  TMEM184A WILD-TYPE   11   18
        clus
vv       TMEM184A MUTATED TMEM184A WILD-TYPE
  FEMALE                3                 11
  MALE                  1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMEM184A MUTATED                                     4
  TMEM184A WILD-TYPE                                  24
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMEM184A MUTATED                                       0
  TMEM184A WILD-TYPE                                     3
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMEM184A MUTATED                                                  0
  TMEM184A WILD-TYPE                                                2
D57V8, multiclass
                                                  clus
vv                                                 TMEM184A MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 TMEM184A WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, continuous
[1] "Remove cluster labels:" "TMEM184A MUTATED"      
clus
  TMEM184A MUTATED TMEM184A WILD-TYPE 
                 2                  9 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H8-A6C1 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A5SS 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-LB-A7SX         TCGA-OE-A75W 
"TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" "TMEM184A WILD-TYPE" 
D57V10, binary
                    cls
clus                  0  1
  TMEM184A MUTATED    4  0
  TMEM184A WILD-TYPE 20  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM184A MUTATED      4    0
  TMEM184A WILD-TYPE   20    9
    clus
vv   TMEM184A MUTATED TMEM184A WILD-TYPE
  R0                4                 20
  R1                0                  9
[1] 2 2
[1] FALSE
D57V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMEM184A MUTATED       0                         0     4
  TMEM184A WILD-TYPE     2                         3    24
D57V12, multiclass
                           clus
vv                          TMEM184A MUTATED TMEM184A WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    4                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = BEGAIN MUTATION ANALYSIS
D58V1, survival
                  sevent
clus2               0  1
  BEGAIN MUTATED    2  1
  BEGAIN WILD-TYPE 16  4
  BEGAIN MUTATED BEGAIN WILD-TYPE 
               3               20 
  BEGAIN MUTATED BEGAIN WILD-TYPE 
               1                4 
$`BEGAIN MUTATED`
TCGA-FB-A7DR TCGA-HZ-7925 TCGA-IB-7651 
         166          361         1989 

$`BEGAIN WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449            1          396           28 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
          11           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  BEGAIN MUTATED BEGAIN WILD-TYPE 
             166                1 
  BEGAIN MUTATED BEGAIN WILD-TYPE 
            1989             1991 
  BEGAIN MUTATED BEGAIN WILD-TYPE 
           361.0            314.5 
[1] "166.0 - 1989.0 (361.0)" "1.0 - 1991.0 (314.5)"  
[1] "hr=" "1.3"
D58V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BEGAIN MUTATED          0         1         3         0        0
  BEGAIN WILD-TYPE        2         5        20         1        1
D58V3, multiclass
           clus
vv          BEGAIN MUTATED BEGAIN WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              1                5
  STAGE IIB              3               20
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  BEGAIN MUTATED          4
  BEGAIN WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D58V5, binary
                  cls
clus                0  1
  BEGAIN MUTATED    0  3
  BEGAIN WILD-TYPE  7 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BEGAIN MUTATED      0    3
  BEGAIN WILD-TYPE    7   22
   clus
vv  BEGAIN MUTATED BEGAIN WILD-TYPE
  0              0                7
  1              3               22
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  BEGAIN MUTATED    2  0  2
  BEGAIN WILD-TYPE 17  1 11
D58V6, multiclass
    clus
vv   BEGAIN MUTATED BEGAIN WILD-TYPE
  M0              2               17
  M1              0                1
  MX              2               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                  cls
clus                0  1
  BEGAIN MUTATED    2  2
  BEGAIN WILD-TYPE 12 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BEGAIN MUTATED      2    2
  BEGAIN WILD-TYPE   12   17
        clus
vv       BEGAIN MUTATED BEGAIN WILD-TYPE
  FEMALE              2               12
  MALE                2               17
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BEGAIN MUTATED                                     3
  BEGAIN WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BEGAIN MUTATED                                       0
  BEGAIN WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BEGAIN MUTATED                                                  1
  BEGAIN WILD-TYPE                                                1
D58V8, multiclass
                                                  clus
vv                                                 BEGAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
                                                  clus
vv                                                 BEGAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  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"
D58V9, continuous
[1] "Remove cluster labels:" "BEGAIN MUTATED"        
clus
  BEGAIN MUTATED BEGAIN WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-H8-A6C1       TCGA-IB-7885 
"BEGAIN WILD-TYPE" "BEGAIN WILD-TYPE" "BEGAIN WILD-TYPE" "BEGAIN WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-LB-A7SX 
"BEGAIN WILD-TYPE" "BEGAIN WILD-TYPE" "BEGAIN WILD-TYPE" "BEGAIN WILD-TYPE" 
      TCGA-OE-A75W 
"BEGAIN WILD-TYPE" 
D58V10, binary
                  cls
clus                0  1
  BEGAIN MUTATED    4  0
  BEGAIN WILD-TYPE 20  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BEGAIN MUTATED      4    0
  BEGAIN WILD-TYPE   20    9
    clus
vv   BEGAIN MUTATED BEGAIN WILD-TYPE
  R0              4               20
  R1              0                9
[1] 2 2
[1] FALSE
D58V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BEGAIN MUTATED       1                         0     3
  BEGAIN WILD-TYPE     1                         3    25
D58V12, multiclass
                           clus
vv                          BEGAIN MUTATED BEGAIN WILD-TYPE
  ASIAN                                  1                1
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = PASD1 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2              0  1
  PASD1 MUTATED    3  2
  PASD1 WILD-TYPE 15  3
  PASD1 MUTATED PASD1 WILD-TYPE 
              5              18 
  PASD1 MUTATED PASD1 WILD-TYPE 
              2               3 
$`PASD1 MUTATED`
TCGA-F2-7273 TCGA-HZ-7918 TCGA-IB-7651 TCGA-OE-A75W TCGA-Q3-A5QY 
         360           28         1989          110          416 

$`PASD1 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7925 
         153          449            1          166          396          361 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
          11           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-US-A776 
         300         1991            8         1968          127          844 

  PASD1 MUTATED PASD1 WILD-TYPE 
             28               1 
  PASD1 MUTATED PASD1 WILD-TYPE 
           1989            1991 
  PASD1 MUTATED PASD1 WILD-TYPE 
          360.0           314.5 
[1] "28.0 - 1989.0 (360.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "2.2"
D59V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PASD1 MUTATED          0         1         4         0        0
  PASD1 WILD-TYPE        2         5        19         1        1
D59V3, multiclass
           clus
vv          PASD1 MUTATED PASD1 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             4              19
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  PASD1 MUTATED          5
  PASD1 WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D59V5, binary
                 cls
clus               0  1
  PASD1 MUTATED    1  4
  PASD1 WILD-TYPE  6 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PASD1 MUTATED      1    4
  PASD1 WILD-TYPE    6   21
   clus
vv  PASD1 MUTATED PASD1 WILD-TYPE
  0             1               6
  1             4              21
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  PASD1 MUTATED    4  0  1
  PASD1 WILD-TYPE 15  1 12
D59V6, multiclass
    clus
vv   PASD1 MUTATED PASD1 WILD-TYPE
  M0             4              15
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                 cls
clus               0  1
  PASD1 MUTATED    1  4
  PASD1 WILD-TYPE 13 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PASD1 MUTATED      1    4
  PASD1 WILD-TYPE   13   15
        clus
vv       PASD1 MUTATED PASD1 WILD-TYPE
  FEMALE             1              13
  MALE               4              15
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PASD1 MUTATED                                     5
  PASD1 WILD-TYPE                                  23
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PASD1 MUTATED                                       0
  PASD1 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PASD1 MUTATED                                                  0
  PASD1 WILD-TYPE                                                2
D59V8, multiclass
                                                  clus
vv                                                 PASD1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PASD1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           23
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, continuous
[1] "Remove cluster labels:" "PASD1 MUTATED"         
clus
  PASD1 MUTATED PASD1 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"PASD1 WILD-TYPE" "PASD1 WILD-TYPE" "PASD1 WILD-TYPE" "PASD1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"PASD1 WILD-TYPE" "PASD1 WILD-TYPE" "PASD1 WILD-TYPE" "PASD1 WILD-TYPE" 
     TCGA-LB-A7SX 
"PASD1 WILD-TYPE" 
D59V10, binary
                 cls
clus               0  1
  PASD1 MUTATED    4  1
  PASD1 WILD-TYPE 20  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PASD1 MUTATED      4    1
  PASD1 WILD-TYPE   20    8
    clus
vv   PASD1 MUTATED PASD1 WILD-TYPE
  R0             4              20
  R1             1               8
[1] 2 2
[1] FALSE
D59V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PASD1 MUTATED       0                         1     4
  PASD1 WILD-TYPE     2                         2    24
D59V12, multiclass
                           clus
vv                          PASD1 MUTATED PASD1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = RBM45 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2              0  1
  RBM45 MUTATED    1  2
  RBM45 WILD-TYPE 17  3
  RBM45 MUTATED RBM45 WILD-TYPE 
              3              20 
  RBM45 MUTATED RBM45 WILD-TYPE 
              2               3 
$`RBM45 MUTATED`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-IB-7651 
         360          449         1989 

$`RBM45 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7925 
         153            1          166          396           28          361 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
          11           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  RBM45 MUTATED RBM45 WILD-TYPE 
            360               1 
  RBM45 MUTATED RBM45 WILD-TYPE 
           1989            1991 
  RBM45 MUTATED RBM45 WILD-TYPE 
            449             233 
[1] "360.0 - 1989.0 (449.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "2.2"
D60V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  RBM45 MUTATED          1         0         3         0        0
  RBM45 WILD-TYPE        1         6        20         1        1
D60V3, multiclass
           clus
vv          RBM45 MUTATED RBM45 WILD-TYPE
  STAGE IB              1               1
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  RBM45 MUTATED          4
  RBM45 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D60V5, binary
                 cls
clus               0  1
  RBM45 MUTATED    1  3
  RBM45 WILD-TYPE  6 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM45 MUTATED      1    3
  RBM45 WILD-TYPE    6   22
   clus
vv  RBM45 MUTATED RBM45 WILD-TYPE
  0             1               6
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  RBM45 MUTATED    3  0  1
  RBM45 WILD-TYPE 16  1 12
D60V6, multiclass
    clus
vv   RBM45 MUTATED RBM45 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                 cls
clus               0  1
  RBM45 MUTATED    1  3
  RBM45 WILD-TYPE 13 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM45 MUTATED      1    3
  RBM45 WILD-TYPE   13   16
        clus
vv       RBM45 MUTATED RBM45 WILD-TYPE
  FEMALE             1              13
  MALE               3              16
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  RBM45 MUTATED                                     3
  RBM45 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  RBM45 MUTATED                                       1
  RBM45 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  RBM45 MUTATED                                                  0
  RBM45 WILD-TYPE                                                2
D60V8, multiclass
                                                  clus
vv                                                 RBM45 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 RBM45 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, continuous
[1] "Remove cluster labels:" "RBM45 MUTATED"         
clus
  RBM45 MUTATED RBM45 WILD-TYPE 
              2               9 
     TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1      TCGA-IB-7885 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" "RBM45 WILD-TYPE" 
     TCGA-OE-A75W 
"RBM45 WILD-TYPE" 
D60V10, binary
                 cls
clus               0  1
  RBM45 MUTATED    2  2
  RBM45 WILD-TYPE 22  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM45 MUTATED      2    2
  RBM45 WILD-TYPE   22    7
    clus
vv   RBM45 MUTATED RBM45 WILD-TYPE
  R0             2              22
  R1             2               7
[1] 2 2
[1] FALSE
D60V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM45 MUTATED       0                         1     3
  RBM45 WILD-TYPE     2                         2    25
D60V12, multiclass
                           clus
vv                          RBM45 MUTATED RBM45 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = POM121 MUTATION ANALYSIS
D61V1, survival
                  sevent
clus2               0  1
  POM121 MUTATED    2  1
  POM121 WILD-TYPE 16  4
  POM121 MUTATED POM121 WILD-TYPE 
               3               20 
  POM121 MUTATED POM121 WILD-TYPE 
               1                4 
$`POM121 MUTATED`
TCGA-H8-A6C1 TCGA-IB-7651 TCGA-Q3-A5QY 
         396         1989          416 

$`POM121 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-US-A776 
         110          844 

  POM121 MUTATED POM121 WILD-TYPE 
             396                1 
  POM121 MUTATED POM121 WILD-TYPE 
            1989             1991 
  POM121 MUTATED POM121 WILD-TYPE 
             416              233 
[1] "396.0 - 1989.0 (416.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D61V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  POM121 MUTATED          1         1         2         0        0
  POM121 WILD-TYPE        1         5        21         1        1
D61V3, multiclass
           clus
vv          POM121 MUTATED POM121 WILD-TYPE
  STAGE IB               1                1
  STAGE IIA              1                5
  STAGE IIB              2               21
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  POM121 MUTATED          4
  POM121 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D61V5, binary
                  cls
clus                0  1
  POM121 MUTATED    2  2
  POM121 WILD-TYPE  5 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      2    2
  POM121 WILD-TYPE    5   23
   clus
vv  POM121 MUTATED POM121 WILD-TYPE
  0              2                5
  1              2               23
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  POM121 MUTATED    2  0  2
  POM121 WILD-TYPE 17  1 11
D61V6, multiclass
    clus
vv   POM121 MUTATED POM121 WILD-TYPE
  M0              2               17
  M1              0                1
  MX              2               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                  cls
clus                0  1
  POM121 MUTATED    2  2
  POM121 WILD-TYPE 12 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      2    2
  POM121 WILD-TYPE   12   17
        clus
vv       POM121 MUTATED POM121 WILD-TYPE
  FEMALE              2               12
  MALE                2               17
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  POM121 MUTATED                                     3
  POM121 WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  POM121 MUTATED                                       1
  POM121 WILD-TYPE                                     2
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  POM121 MUTATED                                                  0
  POM121 WILD-TYPE                                                2
D61V8, multiclass
                                                  clus
vv                                                 POM121 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 POM121 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, continuous
[1] "Remove cluster labels:" "POM121 MUTATED"        
clus
  POM121 MUTATED POM121 WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-IB-7885 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-LB-A7SX 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-OE-A75W 
"POM121 WILD-TYPE" 
D61V10, binary
                  cls
clus                0  1
  POM121 MUTATED    4  0
  POM121 WILD-TYPE 20  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      4    0
  POM121 WILD-TYPE   20    9
    clus
vv   POM121 MUTATED POM121 WILD-TYPE
  R0              4               20
  R1              0                9
[1] 2 2
[1] FALSE
D61V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POM121 MUTATED       0                         0     4
  POM121 WILD-TYPE     2                         3    24
D61V12, multiclass
                           clus
vv                          POM121 MUTATED POM121 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  4               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = EME2 MUTATION ANALYSIS
D62V1, survival
                sevent
clus2             0  1
  EME2 MUTATED    2  1
  EME2 WILD-TYPE 16  4
  EME2 MUTATED EME2 WILD-TYPE 
             3             20 
  EME2 MUTATED EME2 WILD-TYPE 
             1              4 
$`EME2 MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SO 
        1989          851          329 

$`EME2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 
          28          361           11           13          476           17 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  EME2 MUTATED EME2 WILD-TYPE 
           329              1 
  EME2 MUTATED EME2 WILD-TYPE 
          1989           1991 
  EME2 MUTATED EME2 WILD-TYPE 
           851            233 
[1] "329.0 - 1989.0 (851.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.3"
D62V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  EME2 MUTATED          0         0         3         0        0
  EME2 WILD-TYPE        2         6        20         1        1
D62V3, multiclass
           clus
vv          EME2 MUTATED EME2 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            3             20
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  EME2 MUTATED          3
  EME2 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D62V5, binary
                cls
clus              0  1
  EME2 MUTATED    0  3
  EME2 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME2 MUTATED      0    3
  EME2 WILD-TYPE    7   22
   clus
vv  EME2 MUTATED EME2 WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  EME2 MUTATED    3  0  0
  EME2 WILD-TYPE 16  1 13
D62V6, multiclass
    clus
vv   EME2 MUTATED EME2 WILD-TYPE
  M0            3             16
  M1            0              1
  MX            0             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                cls
clus              0  1
  EME2 MUTATED    2  1
  EME2 WILD-TYPE 12 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME2 MUTATED      2    1
  EME2 WILD-TYPE   12   18
        clus
vv       EME2 MUTATED EME2 WILD-TYPE
  FEMALE            2             12
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EME2 MUTATED                                     3
  EME2 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EME2 MUTATED                                       0
  EME2 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EME2 MUTATED                                                  0
  EME2 WILD-TYPE                                                2
D62V8, multiclass
                                                  clus
vv                                                 EME2 MUTATED EME2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D62V9, continuous
[1] "Remove cluster labels:" "EME2 MUTATED"          
clus
  EME2 MUTATED EME2 WILD-TYPE 
             2              9 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"EME2 WILD-TYPE" "EME2 WILD-TYPE" "EME2 WILD-TYPE" "EME2 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG     TCGA-LB-A7SX 
"EME2 WILD-TYPE" "EME2 WILD-TYPE" "EME2 WILD-TYPE" "EME2 WILD-TYPE" 
    TCGA-OE-A75W 
"EME2 WILD-TYPE" 
D62V10, binary
                cls
clus              0  1
  EME2 MUTATED    3  0
  EME2 WILD-TYPE 21  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  EME2 MUTATED      3    0
  EME2 WILD-TYPE   21    9
    clus
vv   EME2 MUTATED EME2 WILD-TYPE
  R0            3             21
  R1            0              9
[1] 2 2
[1] FALSE
D62V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EME2 MUTATED       0                         0     3
  EME2 WILD-TYPE     2                         3    25
D62V12, multiclass
                           clus
vv                          EME2 MUTATED EME2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = CUL4B MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2              0  1
  CUL4B MUTATED    1  1
  CUL4B WILD-TYPE 17  4
  CUL4B MUTATED CUL4B WILD-TYPE 
              2              21 
  CUL4B MUTATED CUL4B WILD-TYPE 
              1               4 
$`CUL4B MUTATED`
TCGA-IB-7651 TCGA-IB-8126 
        1989           17 

$`CUL4B WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  CUL4B MUTATED CUL4B WILD-TYPE 
             17               1 
  CUL4B MUTATED CUL4B WILD-TYPE 
           1989            1991 
  CUL4B MUTATED CUL4B WILD-TYPE 
           1003             329 
[1] "17.0 - 1989.0 (1003.0)" "1.0 - 1991.0 (329.0)"  
[1] "Remove cluster labels:" "CUL4B MUTATED"         
D63V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CUL4B MUTATED          0         0         2         1        0
  CUL4B WILD-TYPE        2         6        21         0        1
D63V3, multiclass
           clus
vv          CUL4B MUTATED CUL4B WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             2              21
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  CUL4B MUTATED          3
  CUL4B WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D63V5, binary
                 cls
clus               0  1
  CUL4B MUTATED    0  3
  CUL4B WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      0    3
  CUL4B WILD-TYPE    7   22
   clus
vv  CUL4B MUTATED CUL4B WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  CUL4B MUTATED    2  0  1
  CUL4B WILD-TYPE 17  1 12
D63V6, multiclass
    clus
vv   CUL4B MUTATED CUL4B WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                 cls
clus               0  1
  CUL4B MUTATED    3  0
  CUL4B WILD-TYPE 11 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      3    0
  CUL4B WILD-TYPE   11   19
        clus
vv       CUL4B MUTATED CUL4B WILD-TYPE
  FEMALE             3              11
  MALE               0              19
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CUL4B MUTATED                                     3
  CUL4B WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CUL4B MUTATED                                       0
  CUL4B WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CUL4B MUTATED                                                  0
  CUL4B WILD-TYPE                                                2
D63V8, multiclass
                                                  clus
vv                                                 CUL4B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CUL4B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, continuous
[1] "Remove cluster labels:" "CUL4B MUTATED"         
clus
  CUL4B MUTATED CUL4B WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"CUL4B WILD-TYPE" "CUL4B WILD-TYPE" "CUL4B WILD-TYPE" "CUL4B WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"CUL4B WILD-TYPE" "CUL4B WILD-TYPE" "CUL4B WILD-TYPE" "CUL4B WILD-TYPE" 
     TCGA-OE-A75W 
"CUL4B WILD-TYPE" 
D63V10, binary
                 cls
clus               0  1
  CUL4B MUTATED    2  1
  CUL4B WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CUL4B MUTATED      2    1
  CUL4B WILD-TYPE   22    8
    clus
vv   CUL4B MUTATED CUL4B WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D63V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CUL4B MUTATED       0                         0     3
  CUL4B WILD-TYPE     2                         3    25
D63V12, multiclass
                           clus
vv                          CUL4B MUTATED CUL4B WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = IFT46 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2              0  1
  IFT46 MUTATED    1  1
  IFT46 WILD-TYPE 17  4
  IFT46 MUTATED IFT46 WILD-TYPE 
              2              21 
  IFT46 MUTATED IFT46 WILD-TYPE 
              1               4 
$`IFT46 MUTATED`
TCGA-IB-7651 TCGA-IB-A5SO 
        1989          329 

$`IFT46 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
          17          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  IFT46 MUTATED IFT46 WILD-TYPE 
            329               1 
  IFT46 MUTATED IFT46 WILD-TYPE 
           1989            1991 
  IFT46 MUTATED IFT46 WILD-TYPE 
           1159             300 
[1] "329.0 - 1989.0 (1159.0)" "1.0 - 1991.0 (300.0)"   
[1] "Remove cluster labels:" "IFT46 MUTATED"         
D64V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  IFT46 MUTATED          0         0         3         0        1
  IFT46 WILD-TYPE        2         6        20         1        0
D64V3, multiclass
           clus
vv          IFT46 MUTATED IFT46 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              1               0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  IFT46 MUTATED          4
  IFT46 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D64V5, binary
                 cls
clus               0  1
  IFT46 MUTATED    0  4
  IFT46 WILD-TYPE  7 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT46 MUTATED      0    4
  IFT46 WILD-TYPE    7   21
   clus
vv  IFT46 MUTATED IFT46 WILD-TYPE
  0             0               7
  1             4              21
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  IFT46 MUTATED    2  1  1
  IFT46 WILD-TYPE 17  0 12
D64V6, multiclass
    clus
vv   IFT46 MUTATED IFT46 WILD-TYPE
  M0             2              17
  M1             1               0
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                 cls
clus               0  1
  IFT46 MUTATED    1  3
  IFT46 WILD-TYPE 13 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT46 MUTATED      1    3
  IFT46 WILD-TYPE   13   16
        clus
vv       IFT46 MUTATED IFT46 WILD-TYPE
  FEMALE             1              13
  MALE               3              16
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IFT46 MUTATED                                     3
  IFT46 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IFT46 MUTATED                                       1
  IFT46 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IFT46 MUTATED                                                  0
  IFT46 WILD-TYPE                                                2
D64V8, multiclass
                                                  clus
vv                                                 IFT46 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 IFT46 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, continuous
[1] "Remove cluster labels:" "IFT46 MUTATED"         
clus
  IFT46 MUTATED IFT46 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"IFT46 WILD-TYPE" "IFT46 WILD-TYPE" 
D64V10, binary
                 cls
clus               0  1
  IFT46 MUTATED    3  1
  IFT46 WILD-TYPE 21  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT46 MUTATED      3    1
  IFT46 WILD-TYPE   21    8
    clus
vv   IFT46 MUTATED IFT46 WILD-TYPE
  R0             3              21
  R1             1               8
[1] 2 2
[1] FALSE
D64V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFT46 MUTATED       0                         0     4
  IFT46 WILD-TYPE     2                         3    24
D64V12, multiclass
                           clus
vv                          IFT46 MUTATED IFT46 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = OTUD4 MUTATION ANALYSIS
D65V1, survival
                 sevent
clus2              0  1
  OTUD4 MUTATED    4  1
  OTUD4 WILD-TYPE 14  4
  OTUD4 MUTATED OTUD4 WILD-TYPE 
              5              18 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
              1               4 
$`OTUD4 MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-A5SP TCGA-Q3-A5QY TCGA-US-A776 
         361         1989          300          416          844 

$`OTUD4 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         329         1991            8         1968          127          110 

  OTUD4 MUTATED OTUD4 WILD-TYPE 
            300               1 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
           1989            1991 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
          416.0           159.5 
[1] "300.0 - 1989.0 (416.0)" "1.0 - 1991.0 (159.5)"  
[1] "hr=" "1.9"
D65V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OTUD4 MUTATED          0         2         3         0        0
  OTUD4 WILD-TYPE        2         4        20         1        1
D65V3, multiclass
           clus
vv          OTUD4 MUTATED OTUD4 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             2               4
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  OTUD4 MUTATED          5
  OTUD4 WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D65V5, binary
                 cls
clus               0  1
  OTUD4 MUTATED    2  3
  OTUD4 WILD-TYPE  5 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED      2    3
  OTUD4 WILD-TYPE    5   22
   clus
vv  OTUD4 MUTATED OTUD4 WILD-TYPE
  0             2               5
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  OTUD4 MUTATED    2  0  3
  OTUD4 WILD-TYPE 17  1 10
D65V6, multiclass
    clus
vv   OTUD4 MUTATED OTUD4 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             3              10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                 cls
clus               0  1
  OTUD4 MUTATED    1  4
  OTUD4 WILD-TYPE 13 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED      1    4
  OTUD4 WILD-TYPE   13   15
        clus
vv       OTUD4 MUTATED OTUD4 WILD-TYPE
  FEMALE             1              13
  MALE               4              15
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OTUD4 MUTATED                                     4
  OTUD4 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OTUD4 MUTATED                                       0
  OTUD4 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OTUD4 MUTATED                                                  1
  OTUD4 WILD-TYPE                                                1
D65V8, multiclass
                                                  clus
vv                                                 OTUD4 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 OTUD4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, continuous
[1] "Remove cluster labels:" "OTUD4 MUTATED"         
clus
  OTUD4 MUTATED OTUD4 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"OTUD4 WILD-TYPE" "OTUD4 WILD-TYPE" "OTUD4 WILD-TYPE" "OTUD4 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"OTUD4 WILD-TYPE" "OTUD4 WILD-TYPE" "OTUD4 WILD-TYPE" "OTUD4 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"OTUD4 WILD-TYPE" "OTUD4 WILD-TYPE" 
D65V10, binary
                 cls
clus               0  1
  OTUD4 MUTATED    4  1
  OTUD4 WILD-TYPE 20  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED      4    1
  OTUD4 WILD-TYPE   20    8
    clus
vv   OTUD4 MUTATED OTUD4 WILD-TYPE
  R0             4              20
  R1             1               8
[1] 2 2
[1] FALSE
D65V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTUD4 MUTATED       0                         0     5
  OTUD4 WILD-TYPE     2                         3    23
D65V12, multiclass
                           clus
vv                          OTUD4 MUTATED OTUD4 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 5              23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = GABBR1 MUTATION ANALYSIS
D66V1, survival
                  sevent
clus2               0  1
  GABBR1 MUTATED    2  1
  GABBR1 WILD-TYPE 16  4
  GABBR1 MUTATED GABBR1 WILD-TYPE 
               3               20 
  GABBR1 MUTATED GABBR1 WILD-TYPE 
               1                4 
$`GABBR1 MUTATED`
TCGA-IB-7651 TCGA-IB-8126 TCGA-US-A776 
        1989           17          844 

$`GABBR1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY 
         110          416 

  GABBR1 MUTATED GABBR1 WILD-TYPE 
              17                1 
  GABBR1 MUTATED GABBR1 WILD-TYPE 
            1989             1991 
  GABBR1 MUTATED GABBR1 WILD-TYPE 
           844.0            314.5 
[1] "17.0 - 1989.0 (844.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.2"
D66V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GABBR1 MUTATED          0         1         2         1        0
  GABBR1 WILD-TYPE        2         5        21         0        1
D66V3, multiclass
           clus
vv          GABBR1 MUTATED GABBR1 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              1                5
  STAGE IIB              2               21
  STAGE III              1                0
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  GABBR1 MUTATED          4
  GABBR1 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D66V5, binary
                  cls
clus                0  1
  GABBR1 MUTATED    1  3
  GABBR1 WILD-TYPE  6 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABBR1 MUTATED      1    3
  GABBR1 WILD-TYPE    6   22
   clus
vv  GABBR1 MUTATED GABBR1 WILD-TYPE
  0              1                6
  1              3               22
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  GABBR1 MUTATED    2  0  2
  GABBR1 WILD-TYPE 17  1 11
D66V6, multiclass
    clus
vv   GABBR1 MUTATED GABBR1 WILD-TYPE
  M0              2               17
  M1              0                1
  MX              2               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                  cls
clus                0  1
  GABBR1 MUTATED    2  2
  GABBR1 WILD-TYPE 12 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABBR1 MUTATED      2    2
  GABBR1 WILD-TYPE   12   17
        clus
vv       GABBR1 MUTATED GABBR1 WILD-TYPE
  FEMALE              2               12
  MALE                2               17
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GABBR1 MUTATED                                     2
  GABBR1 WILD-TYPE                                  26
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GABBR1 MUTATED                                       1
  GABBR1 WILD-TYPE                                     2
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GABBR1 MUTATED                                                  1
  GABBR1 WILD-TYPE                                                1
D66V8, multiclass
                                                  clus
vv                                                 GABBR1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              1
                                                  clus
vv                                                 GABBR1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  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"
D66V9, continuous
[1] "Remove cluster labels:" "GABBR1 MUTATED"        
clus
  GABBR1 MUTATED GABBR1 WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-H8-A6C1 
"GABBR1 WILD-TYPE" "GABBR1 WILD-TYPE" "GABBR1 WILD-TYPE" "GABBR1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-LB-A7SX 
"GABBR1 WILD-TYPE" "GABBR1 WILD-TYPE" "GABBR1 WILD-TYPE" "GABBR1 WILD-TYPE" 
      TCGA-OE-A75W 
"GABBR1 WILD-TYPE" 
D66V10, binary
                  cls
clus                0  1
  GABBR1 MUTATED    2  2
  GABBR1 WILD-TYPE 22  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABBR1 MUTATED      2    2
  GABBR1 WILD-TYPE   22    7
    clus
vv   GABBR1 MUTATED GABBR1 WILD-TYPE
  R0              2               22
  R1              2                7
[1] 2 2
[1] FALSE
D66V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GABBR1 MUTATED       0                         0     4
  GABBR1 WILD-TYPE     2                         3    24
D66V12, multiclass
                           clus
vv                          GABBR1 MUTATED GABBR1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  4               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = MYH10 MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2              0  1
  MYH10 MUTATED    0  3
  MYH10 WILD-TYPE 18  2
  MYH10 MUTATED MYH10 WILD-TYPE 
              3              20 
  MYH10 MUTATED MYH10 WILD-TYPE 
              3               2 
$`MYH10 MUTATED`
TCGA-F2-7273 TCGA-F2-A44G TCGA-IB-7651 
         360          153         1989 

$`MYH10 WILD-TYPE`
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7925 
         449            1          166          396           28          361 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
          11           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  MYH10 MUTATED MYH10 WILD-TYPE 
            153               1 
  MYH10 MUTATED MYH10 WILD-TYPE 
           1989            1991 
  MYH10 MUTATED MYH10 WILD-TYPE 
          360.0           314.5 
[1] "153.0 - 1989.0 (360.0)" "1.0 - 1991.0 (314.5)"  
[1] "hr=" "8.1"
D67V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MYH10 MUTATED          0         0         4         0        0
  MYH10 WILD-TYPE        2         6        19         1        1
D67V3, multiclass
           clus
vv          MYH10 MUTATED MYH10 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             4              19
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  MYH10 MUTATED          4
  MYH10 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D67V5, binary
                 cls
clus               0  1
  MYH10 MUTATED    0  4
  MYH10 WILD-TYPE  7 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH10 MUTATED      0    4
  MYH10 WILD-TYPE    7   21
   clus
vv  MYH10 MUTATED MYH10 WILD-TYPE
  0             0               7
  1             4              21
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  MYH10 MUTATED    3  0  1
  MYH10 WILD-TYPE 16  1 12
D67V6, multiclass
    clus
vv   MYH10 MUTATED MYH10 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                 cls
clus               0  1
  MYH10 MUTATED    3  1
  MYH10 WILD-TYPE 11 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH10 MUTATED      3    1
  MYH10 WILD-TYPE   11   18
        clus
vv       MYH10 MUTATED MYH10 WILD-TYPE
  FEMALE             3              11
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MYH10 MUTATED                                     4
  MYH10 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MYH10 MUTATED                                       0
  MYH10 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MYH10 MUTATED                                                  0
  MYH10 WILD-TYPE                                                2
D67V8, multiclass
                                                  clus
vv                                                 MYH10 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 MYH10 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, continuous
[1] "Remove cluster labels:" "MYH10 MUTATED"         
clus
  MYH10 MUTATED MYH10 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"MYH10 WILD-TYPE" "MYH10 WILD-TYPE" "MYH10 WILD-TYPE" "MYH10 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"MYH10 WILD-TYPE" "MYH10 WILD-TYPE" "MYH10 WILD-TYPE" "MYH10 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"MYH10 WILD-TYPE" "MYH10 WILD-TYPE" 
D67V10, binary
                 cls
clus               0  1
  MYH10 MUTATED    2  2
  MYH10 WILD-TYPE 22  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH10 MUTATED      2    2
  MYH10 WILD-TYPE   22    7
    clus
vv   MYH10 MUTATED MYH10 WILD-TYPE
  R0             2              22
  R1             2               7
[1] 2 2
[1] FALSE
D67V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYH10 MUTATED       0                         1     3
  MYH10 WILD-TYPE     2                         2    25
D67V12, multiclass
                           clus
vv                          MYH10 MUTATED MYH10 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = ERF MUTATION ANALYSIS
D68V1, survival
               sevent
clus2            0  1
  ERF MUTATED    2  2
  ERF WILD-TYPE 16  3
  ERF MUTATED ERF WILD-TYPE 
            4            19 
  ERF MUTATED ERF WILD-TYPE 
            2             3 
$`ERF MUTATED`
TCGA-F2-7273 TCGA-IB-7651 TCGA-IB-8126 TCGA-OE-A75W 
         360         1989           17          110 

$`ERF WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
         361           11           13          476          851          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-Q3-A5QY 
         300         1991            8         1968          127          416 
TCGA-US-A776 
         844 

  ERF MUTATED ERF WILD-TYPE 
           17             1 
  ERF MUTATED ERF WILD-TYPE 
         1989          1991 
  ERF MUTATED ERF WILD-TYPE 
          235           329 
[1] "17.0 - 1989.0 (235.0)" "1.0 - 1991.0 (329.0)" 
[1] "hr=" "2.8"
D68V2, continuous
               vv
clus            STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ERF MUTATED          0         1         2         1        0
  ERF WILD-TYPE        2         5        21         0        1
D68V3, multiclass
           clus
vv          ERF MUTATED ERF WILD-TYPE
  STAGE IB            0             2
  STAGE IIA           1             5
  STAGE IIB           2            21
  STAGE III           1             0
  STAGE IV            0             1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T2+T3+T4
  ERF MUTATED          4
  ERF WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D68V5, binary
               cls
clus             0  1
  ERF MUTATED    1  3
  ERF WILD-TYPE  6 22
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      1    3
  ERF WILD-TYPE    6   22
   clus
vv  ERF MUTATED ERF WILD-TYPE
  0           1             6
  1           3            22
[1] 2 2
[1] FALSE
               vv
clus            M0 M1 MX
  ERF MUTATED    4  0  0
  ERF WILD-TYPE 15  1 13
D68V6, multiclass
    clus
vv   ERF MUTATED ERF WILD-TYPE
  M0           4            15
  M1           0             1
  MX           0            13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
               cls
clus             0  1
  ERF MUTATED    2  2
  ERF WILD-TYPE 12 17
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      2    2
  ERF WILD-TYPE   12   17
        clus
vv       ERF MUTATED ERF WILD-TYPE
  FEMALE           2            12
  MALE             2            17
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ERF MUTATED                                     4
  ERF WILD-TYPE                                  24
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ERF MUTATED                                       0
  ERF WILD-TYPE                                     3
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ERF MUTATED                                                  0
  ERF WILD-TYPE                                                2
D68V8, multiclass
                                                  clus
vv                                                 ERF MUTATED ERF WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        4            24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0             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"
D68V9, continuous
D68V10, binary
               cls
clus             0  1
  ERF MUTATED    2  2
  ERF WILD-TYPE 22  7
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      2    2
  ERF WILD-TYPE   22    7
    clus
vv   ERF MUTATED ERF WILD-TYPE
  R0           2            22
  R1           2             7
[1] 2 2
[1] FALSE
D68V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERF MUTATED       0                         1     3
  ERF WILD-TYPE     2                         2    25
D68V12, multiclass
                           clus
vv                          ERF MUTATED ERF WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           1             2
  WHITE                               3            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = OR10A7 MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2               0  1
  OR10A7 MUTATED    1  1
  OR10A7 WILD-TYPE 17  4
  OR10A7 MUTATED OR10A7 WILD-TYPE 
               2               21 
  OR10A7 MUTATED OR10A7 WILD-TYPE 
               1                4 
$`OR10A7 MUTATED`
TCGA-F2-A44G TCGA-FB-A78T 
         153            1 

$`OR10A7 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7925 
         360          449          166          396           28          361 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          11           13         1989          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  OR10A7 MUTATED OR10A7 WILD-TYPE 
               1                8 
  OR10A7 MUTATED OR10A7 WILD-TYPE 
             153             1991 
  OR10A7 MUTATED OR10A7 WILD-TYPE 
              77              360 
[1] "1.0 - 153.0 (77.0)"   "8.0 - 1991.0 (360.0)"
[1] "Remove cluster labels:" "OR10A7 MUTATED"        
D69V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OR10A7 MUTATED          0         1         2         0        0
  OR10A7 WILD-TYPE        2         5        21         1        1
D69V3, multiclass
           clus
vv          OR10A7 MUTATED OR10A7 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              1                5
  STAGE IIB              2               21
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  OR10A7 MUTATED          3
  OR10A7 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D69V5, binary
                  cls
clus                0  1
  OR10A7 MUTATED    1  2
  OR10A7 WILD-TYPE  6 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A7 MUTATED      1    2
  OR10A7 WILD-TYPE    6   23
   clus
vv  OR10A7 MUTATED OR10A7 WILD-TYPE
  0              1                6
  1              2               23
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  OR10A7 MUTATED    3  0  0
  OR10A7 WILD-TYPE 16  1 13
D69V6, multiclass
    clus
vv   OR10A7 MUTATED OR10A7 WILD-TYPE
  M0              3               16
  M1              0                1
  MX              0               13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                  cls
clus                0  1
  OR10A7 MUTATED    2  1
  OR10A7 WILD-TYPE 12 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A7 MUTATED      2    1
  OR10A7 WILD-TYPE   12   18
        clus
vv       OR10A7 MUTATED OR10A7 WILD-TYPE
  FEMALE              2               12
  MALE                1               18
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OR10A7 MUTATED                                     3
  OR10A7 WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OR10A7 MUTATED                                       0
  OR10A7 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OR10A7 MUTATED                                                  0
  OR10A7 WILD-TYPE                                                2
D69V8, multiclass
                                                  clus
vv                                                 OR10A7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 OR10A7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, continuous
[1] "Remove cluster labels:" "OR10A7 MUTATED"        
clus
  OR10A7 MUTATED OR10A7 WILD-TYPE 
               1               10 
      TCGA-FB-A5VM       TCGA-FB-A7DR       TCGA-H8-A6C1       TCGA-IB-7651 
"OR10A7 WILD-TYPE" "OR10A7 WILD-TYPE" "OR10A7 WILD-TYPE" "OR10A7 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A5SS       TCGA-IB-A6UG 
"OR10A7 WILD-TYPE" "OR10A7 WILD-TYPE" "OR10A7 WILD-TYPE" "OR10A7 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-OE-A75W 
"OR10A7 WILD-TYPE" "OR10A7 WILD-TYPE" 
D69V10, binary
                  cls
clus                0  1
  OR10A7 MUTATED    2  1
  OR10A7 WILD-TYPE 22  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10A7 MUTATED      2    1
  OR10A7 WILD-TYPE   22    8
    clus
vv   OR10A7 MUTATED OR10A7 WILD-TYPE
  R0              2               22
  R1              1                8
[1] 2 2
[1] FALSE
D69V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR10A7 MUTATED       0                         0     3
  OR10A7 WILD-TYPE     2                         3    25
D69V12, multiclass
                           clus
vv                          OR10A7 MUTATED OR10A7 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = BRDT MUTATION ANALYSIS
D70V1, survival
                sevent
clus2             0  1
  BRDT MUTATED    0  2
  BRDT WILD-TYPE 18  3
  BRDT MUTATED BRDT WILD-TYPE 
             2             21 
  BRDT MUTATED BRDT WILD-TYPE 
             2              3 
$`BRDT MUTATED`
TCGA-F2-7273 TCGA-IB-7651 
         360         1989 

$`BRDT WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  BRDT MUTATED BRDT WILD-TYPE 
           360              1 
  BRDT MUTATED BRDT WILD-TYPE 
          1989           1991 
  BRDT MUTATED BRDT WILD-TYPE 
        1174.5          300.0 
[1] "360.0 - 1989.0 (1174.5)" "1.0 - 1991.0 (300.0)"   
[1] "Remove cluster labels:" "BRDT MUTATED"          
D70V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  BRDT MUTATED          0         0         4         0        0
  BRDT WILD-TYPE        2         6        19         1        1
D70V3, multiclass
           clus
vv          BRDT MUTATED BRDT WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            4             19
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  BRDT MUTATED          4
  BRDT WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D70V5, binary
                cls
clus              0  1
  BRDT MUTATED    0  4
  BRDT WILD-TYPE  7 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      0    4
  BRDT WILD-TYPE    7   21
   clus
vv  BRDT MUTATED BRDT WILD-TYPE
  0            0              7
  1            4             21
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  BRDT MUTATED    2  0  2
  BRDT WILD-TYPE 17  1 11
D70V6, multiclass
    clus
vv   BRDT MUTATED BRDT WILD-TYPE
  M0            2             17
  M1            0              1
  MX            2             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                cls
clus              0  1
  BRDT MUTATED    2  2
  BRDT WILD-TYPE 12 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      2    2
  BRDT WILD-TYPE   12   17
        clus
vv       BRDT MUTATED BRDT WILD-TYPE
  FEMALE            2             12
  MALE              2             17
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  BRDT MUTATED                                     3
  BRDT WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  BRDT MUTATED                                       1
  BRDT WILD-TYPE                                     2
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  BRDT MUTATED                                                  0
  BRDT WILD-TYPE                                                2
D70V8, multiclass
                                                  clus
vv                                                 BRDT MUTATED BRDT WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1              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"
D70V9, continuous
[1] "Remove cluster labels:" "BRDT MUTATED"          
clus
  BRDT MUTATED BRDT WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" "BRDT WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"BRDT WILD-TYPE" "BRDT WILD-TYPE" 
D70V10, binary
                cls
clus              0  1
  BRDT MUTATED    2  2
  BRDT WILD-TYPE 22  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRDT MUTATED      2    2
  BRDT WILD-TYPE   22    7
    clus
vv   BRDT MUTATED BRDT WILD-TYPE
  R0            2             22
  R1            2              7
[1] 2 2
[1] FALSE
D70V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRDT MUTATED       0                         1     3
  BRDT WILD-TYPE     2                         2    25
D70V12, multiclass
                           clus
vv                          BRDT MUTATED BRDT WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = CDHR5 MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2              0  1
  CDHR5 MUTATED    2  0
  CDHR5 WILD-TYPE 16  5
  CDHR5 MUTATED CDHR5 WILD-TYPE 
              2              21 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
              0               5 
$`CDHR5 MUTATED`
TCGA-IB-8126 TCGA-IB-A5SP 
          17          300 

$`CDHR5 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 
          28          361           11           13         1989          476 
TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         851          329         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  CDHR5 MUTATED CDHR5 WILD-TYPE 
             17               1 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
            300            1991 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
          158.5           360.0 
[1] "17.0 - 300.0 (158.5)" "1.0 - 1991.0 (360.0)"
[1] "Remove cluster labels:" "CDHR5 MUTATED"         
D71V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CDHR5 MUTATED          1         1         1         1        0
  CDHR5 WILD-TYPE        1         5        22         0        1
D71V3, multiclass
           clus
vv          CDHR5 MUTATED CDHR5 WILD-TYPE
  STAGE IB              1               1
  STAGE IIA             1               5
  STAGE IIB             1              22
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  CDHR5 MUTATED          4
  CDHR5 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D71V5, binary
                 cls
clus               0  1
  CDHR5 MUTATED    2  2
  CDHR5 WILD-TYPE  5 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      2    2
  CDHR5 WILD-TYPE    5   23
   clus
vv  CDHR5 MUTATED CDHR5 WILD-TYPE
  0             2               5
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  CDHR5 MUTATED    3  0  1
  CDHR5 WILD-TYPE 16  1 12
D71V6, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                 cls
clus               0  1
  CDHR5 MUTATED    3  1
  CDHR5 WILD-TYPE 11 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      3    1
  CDHR5 WILD-TYPE   11   18
        clus
vv       CDHR5 MUTATED CDHR5 WILD-TYPE
  FEMALE             3              11
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CDHR5 MUTATED                                     4
  CDHR5 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CDHR5 MUTATED                                       0
  CDHR5 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CDHR5 MUTATED                                                  0
  CDHR5 WILD-TYPE                                                2
D71V8, multiclass
                                                  clus
vv                                                 CDHR5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CDHR5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, continuous
[1] "Remove cluster labels:" "CDHR5 MUTATED"         
clus
  CDHR5 MUTATED CDHR5 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"CDHR5 WILD-TYPE" "CDHR5 WILD-TYPE" "CDHR5 WILD-TYPE" "CDHR5 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-A5SS      TCGA-IB-A6UG 
"CDHR5 WILD-TYPE" "CDHR5 WILD-TYPE" "CDHR5 WILD-TYPE" "CDHR5 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"CDHR5 WILD-TYPE" "CDHR5 WILD-TYPE" 
D71V10, binary
                 cls
clus               0  1
  CDHR5 MUTATED    2  2
  CDHR5 WILD-TYPE 22  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      2    2
  CDHR5 WILD-TYPE   22    7
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  R0             2              22
  R1             2               7
[1] 2 2
[1] FALSE
D71V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDHR5 MUTATED       0                         0     4
  CDHR5 WILD-TYPE     2                         3    24
D71V12, multiclass
                           clus
vv                          CDHR5 MUTATED CDHR5 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = GPR25 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2              0  1
  GPR25 MUTATED    2  1
  GPR25 WILD-TYPE 16  4
  GPR25 MUTATED GPR25 WILD-TYPE 
              3              20 
  GPR25 MUTATED GPR25 WILD-TYPE 
              1               4 
$`GPR25 MUTATED`
TCGA-H8-A6C1 TCGA-HZ-A77O TCGA-IB-7651 
         396           11         1989 

$`GPR25 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
         361           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  GPR25 MUTATED GPR25 WILD-TYPE 
             11               1 
  GPR25 MUTATED GPR25 WILD-TYPE 
           1989            1991 
  GPR25 MUTATED GPR25 WILD-TYPE 
          396.0           314.5 
[1] "11.0 - 1989.0 (396.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.2"
D72V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GPR25 MUTATED          0         1         2         0        0
  GPR25 WILD-TYPE        2         5        21         1        1
D72V3, multiclass
           clus
vv          GPR25 MUTATED GPR25 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  GPR25 MUTATED          3
  GPR25 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D72V5, binary
                 cls
clus               0  1
  GPR25 MUTATED    1  2
  GPR25 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR25 MUTATED      1    2
  GPR25 WILD-TYPE    6   23
   clus
vv  GPR25 MUTATED GPR25 WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  GPR25 MUTATED    1  0  2
  GPR25 WILD-TYPE 18  1 11
D72V6, multiclass
    clus
vv   GPR25 MUTATED GPR25 WILD-TYPE
  M0             1              18
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                 cls
clus               0  1
  GPR25 MUTATED    2  1
  GPR25 WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR25 MUTATED      2    1
  GPR25 WILD-TYPE   12   18
        clus
vv       GPR25 MUTATED GPR25 WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GPR25 MUTATED                                     2
  GPR25 WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GPR25 MUTATED                                       1
  GPR25 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GPR25 MUTATED                                                  0
  GPR25 WILD-TYPE                                                2
D72V8, multiclass
                                                  clus
vv                                                 GPR25 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 GPR25 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, continuous
[1] "Remove cluster labels:" "GPR25 MUTATED"         
clus
  GPR25 MUTATED GPR25 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-IB-7885 
"GPR25 WILD-TYPE" "GPR25 WILD-TYPE" "GPR25 WILD-TYPE" "GPR25 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"GPR25 WILD-TYPE" "GPR25 WILD-TYPE" "GPR25 WILD-TYPE" "GPR25 WILD-TYPE" 
     TCGA-OE-A75W 
"GPR25 WILD-TYPE" 
D72V10, binary
                 cls
clus               0  1
  GPR25 MUTATED    3  0
  GPR25 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR25 MUTATED      3    0
  GPR25 WILD-TYPE   21    9
    clus
vv   GPR25 MUTATED GPR25 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D72V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR25 MUTATED       0                         0     3
  GPR25 WILD-TYPE     2                         3    25
D72V12, multiclass
                           clus
vv                          GPR25 MUTATED GPR25 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = PPARGC1B MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  PPARGC1B MUTATED    1  1
  PPARGC1B WILD-TYPE 17  4
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 2                 21 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 1                  4 
$`PPARGC1B MUTATED`
TCGA-HZ-7918 TCGA-IB-7651 
          28         1989 

$`PPARGC1B WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                28                  1 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
              1989               1991 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
            1008.5              329.0 
[1] "28.0 - 1989.0 (1008.5)" "1.0 - 1991.0 (329.0)"  
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
D73V2, continuous
                    vv
clus                 STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PPARGC1B MUTATED          0         0         3         0        0
  PPARGC1B WILD-TYPE        2         6        20         1        1
D73V3, multiclass
           clus
vv          PPARGC1B MUTATED PPARGC1B WILD-TYPE
  STAGE IB                 0                  2
  STAGE IIA                0                  6
  STAGE IIB                3                 20
  STAGE III                0                  1
  STAGE IV                 0                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T2+T3+T4
  PPARGC1B MUTATED          3
  PPARGC1B WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D73V5, binary
                    cls
clus                  0  1
  PPARGC1B MUTATED    0  3
  PPARGC1B WILD-TYPE  7 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      0    3
  PPARGC1B WILD-TYPE    7   22
   clus
vv  PPARGC1B MUTATED PPARGC1B WILD-TYPE
  0                0                  7
  1                3                 22
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  PPARGC1B MUTATED    2  0  1
  PPARGC1B WILD-TYPE 17  1 12
D73V6, multiclass
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  M0                2                 17
  M1                0                  1
  MX                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                  0  1
  PPARGC1B MUTATED    2  1
  PPARGC1B WILD-TYPE 12 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      2    1
  PPARGC1B WILD-TYPE   12   18
        clus
vv       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  FEMALE                2                 12
  MALE                  1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PPARGC1B MUTATED                                     3
  PPARGC1B WILD-TYPE                                  25
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PPARGC1B MUTATED                                       0
  PPARGC1B WILD-TYPE                                     3
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PPARGC1B MUTATED                                                  0
  PPARGC1B WILD-TYPE                                                2
D73V8, multiclass
                                                  clus
vv                                                 PPARGC1B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 PPARGC1B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, continuous
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
clus
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 1                 10 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-A7DR 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-IB-7885         TCGA-IB-8126 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UG         TCGA-LB-A7SX 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-OE-A75W 
"PPARGC1B WILD-TYPE" 
D73V10, binary
                    cls
clus                  0  1
  PPARGC1B MUTATED    3  0
  PPARGC1B WILD-TYPE 21  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      3    0
  PPARGC1B WILD-TYPE   21    9
    clus
vv   PPARGC1B MUTATED PPARGC1B WILD-TYPE
  R0                3                 21
  R1                0                  9
[1] 2 2
[1] FALSE
D73V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPARGC1B MUTATED       0                         0     3
  PPARGC1B WILD-TYPE     2                         3    25
D73V12, multiclass
                           clus
vv                          PPARGC1B MUTATED PPARGC1B WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    3                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = SALL1 MUTATION ANALYSIS
D74V1, survival
                 sevent
clus2              0  1
  SALL1 MUTATED    2  1
  SALL1 WILD-TYPE 16  4
  SALL1 MUTATED SALL1 WILD-TYPE 
              3              20 
  SALL1 MUTATED SALL1 WILD-TYPE 
              1               4 
$`SALL1 MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-8126 
        1989          851           17 

$`SALL1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-A5SO 
          28          361           11           13          476          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  SALL1 MUTATED SALL1 WILD-TYPE 
             17               1 
  SALL1 MUTATED SALL1 WILD-TYPE 
           1989            1991 
  SALL1 MUTATED SALL1 WILD-TYPE 
          851.0           314.5 
[1] "17.0 - 1989.0 (851.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.2"
D74V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SALL1 MUTATED          0         0         3         1        0
  SALL1 WILD-TYPE        2         6        20         0        1
D74V3, multiclass
           clus
vv          SALL1 MUTATED SALL1 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  SALL1 MUTATED          4
  SALL1 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D74V5, binary
                 cls
clus               0  1
  SALL1 MUTATED    0  4
  SALL1 WILD-TYPE  7 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      0    4
  SALL1 WILD-TYPE    7   21
   clus
vv  SALL1 MUTATED SALL1 WILD-TYPE
  0             0               7
  1             4              21
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  SALL1 MUTATED    3  0  1
  SALL1 WILD-TYPE 16  1 12
D74V6, multiclass
    clus
vv   SALL1 MUTATED SALL1 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                 cls
clus               0  1
  SALL1 MUTATED    3  1
  SALL1 WILD-TYPE 11 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      3    1
  SALL1 WILD-TYPE   11   18
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  FEMALE             3              11
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SALL1 MUTATED                                     4
  SALL1 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SALL1 MUTATED                                       0
  SALL1 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SALL1 MUTATED                                                  0
  SALL1 WILD-TYPE                                                2
D74V8, multiclass
                                                  clus
vv                                                 SALL1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SALL1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, continuous
D74V10, binary
                 cls
clus               0  1
  SALL1 MUTATED    2  2
  SALL1 WILD-TYPE 22  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      2    2
  SALL1 WILD-TYPE   22    7
    clus
vv   SALL1 MUTATED SALL1 WILD-TYPE
  R0             2              22
  R1             2               7
[1] 2 2
[1] FALSE
D74V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SALL1 MUTATED       0                         0     4
  SALL1 WILD-TYPE     2                         3    24
D74V12, multiclass
                           clus
vv                          SALL1 MUTATED SALL1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = VEPH1 MUTATION ANALYSIS
D75V1, survival
                 sevent
clus2              0  1
  VEPH1 MUTATED    3  1
  VEPH1 WILD-TYPE 15  4
  VEPH1 MUTATED VEPH1 WILD-TYPE 
              4              19 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
              1               4 
$`VEPH1 MUTATED`
TCGA-FB-A78T TCGA-H8-A6C1 TCGA-IB-7651 TCGA-IB-7885 
           1          396         1989          851 

$`VEPH1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-HZ-7918 TCGA-HZ-7925 
         360          153          449          166           28          361 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
          11           13          476           17          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY 
        1991            8         1968          127          110          416 
TCGA-US-A776 
         844 

  VEPH1 MUTATED VEPH1 WILD-TYPE 
              1               8 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
           1989            1991 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
          623.5           300.0 
[1] "1.0 - 1989.0 (623.5)" "8.0 - 1991.0 (300.0)"
[1] "hr=" "1.5"
D75V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  VEPH1 MUTATED          0         1         3         0        0
  VEPH1 WILD-TYPE        2         5        20         1        1
D75V3, multiclass
           clus
vv          VEPH1 MUTATED VEPH1 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  VEPH1 MUTATED          4
  VEPH1 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D75V5, binary
                 cls
clus               0  1
  VEPH1 MUTATED    1  3
  VEPH1 WILD-TYPE  6 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED      1    3
  VEPH1 WILD-TYPE    6   22
   clus
vv  VEPH1 MUTATED VEPH1 WILD-TYPE
  0             1               6
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  VEPH1 MUTATED    3  0  1
  VEPH1 WILD-TYPE 16  1 12
D75V6, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                 cls
clus               0  1
  VEPH1 MUTATED    3  1
  VEPH1 WILD-TYPE 11 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED      3    1
  VEPH1 WILD-TYPE   11   18
        clus
vv       VEPH1 MUTATED VEPH1 WILD-TYPE
  FEMALE             3              11
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  VEPH1 MUTATED                                     3
  VEPH1 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  VEPH1 MUTATED                                       1
  VEPH1 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  VEPH1 MUTATED                                                  0
  VEPH1 WILD-TYPE                                                2
D75V8, multiclass
                                                  clus
vv                                                 VEPH1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 VEPH1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, continuous
D75V10, binary
                 cls
clus               0  1
  VEPH1 MUTATED    4  0
  VEPH1 WILD-TYPE 20  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED      4    0
  VEPH1 WILD-TYPE   20    9
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  R0             4              20
  R1             0               9
[1] 2 2
[1] FALSE
D75V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VEPH1 MUTATED       0                         0     4
  VEPH1 WILD-TYPE     2                         3    24
D75V12, multiclass
                           clus
vv                          VEPH1 MUTATED VEPH1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = ST6GALNAC5 MUTATION ANALYSIS
D76V1, survival
                      sevent
clus2                   0  1
  ST6GALNAC5 MUTATED    2  1
  ST6GALNAC5 WILD-TYPE 16  4
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                   3                   20 
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                   1                    4 
$`ST6GALNAC5 MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-A5ST 
         361         1989            8 

$`ST6GALNAC5 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         329          300         1991         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                   8                    1 
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                1989                 1991 
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
               361.0                314.5 
[1] "8.0 - 1989.0 (361.0)" "1.0 - 1991.0 (314.5)"
[1] "hr=" "1.2"
D76V2, continuous
                      vv
clus                   STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ST6GALNAC5 MUTATED          0         0         3         0        0
  ST6GALNAC5 WILD-TYPE        2         6        20         1        1
D76V3, multiclass
           clus
vv          ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  STAGE IB                   0                    2
  STAGE IIA                  0                    6
  STAGE IIB                  3                   20
  STAGE III                  0                    1
  STAGE IV                   0                    1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   T2+T3+T4
  ST6GALNAC5 MUTATED          3
  ST6GALNAC5 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D76V5, binary
                      cls
clus                    0  1
  ST6GALNAC5 MUTATED    0  3
  ST6GALNAC5 WILD-TYPE  7 22
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC5 MUTATED      0    3
  ST6GALNAC5 WILD-TYPE    7   22
   clus
vv  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  0                  0                    7
  1                  3                   22
[1] 2 2
[1] FALSE
                      vv
clus                   M0 M1 MX
  ST6GALNAC5 MUTATED    2  0  1
  ST6GALNAC5 WILD-TYPE 17  1 12
D76V6, multiclass
    clus
vv   ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  M0                  2                   17
  M1                  0                    1
  MX                  1                   12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                      cls
clus                    0  1
  ST6GALNAC5 MUTATED    2  1
  ST6GALNAC5 WILD-TYPE 12 18
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC5 MUTATED      2    1
  ST6GALNAC5 WILD-TYPE   12   18
        clus
vv       ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  FEMALE                  2                   12
  MALE                    1                   18
[1] 2 2
[1] FALSE
                      vv
clus                   PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ST6GALNAC5 MUTATED                                     3
  ST6GALNAC5 WILD-TYPE                                  25
                      vv
clus                   PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ST6GALNAC5 MUTATED                                       0
  ST6GALNAC5 WILD-TYPE                                     3
                      vv
clus                   PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ST6GALNAC5 MUTATED                                                  0
  ST6GALNAC5 WILD-TYPE                                                2
D76V8, multiclass
                                                  clus
vv                                                 ST6GALNAC5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                               3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  0
                                                  clus
vv                                                 ST6GALNAC5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                               3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                    2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, continuous
[1] "Remove cluster labels:" "ST6GALNAC5 MUTATED"    
clus
  ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE 
                   1                   10 
          TCGA-FB-A5VM           TCGA-FB-A78T           TCGA-FB-A7DR 
"ST6GALNAC5 WILD-TYPE" "ST6GALNAC5 WILD-TYPE" "ST6GALNAC5 WILD-TYPE" 
          TCGA-H8-A6C1           TCGA-IB-7885           TCGA-IB-8126 
"ST6GALNAC5 WILD-TYPE" "ST6GALNAC5 WILD-TYPE" "ST6GALNAC5 WILD-TYPE" 
          TCGA-IB-A5SS           TCGA-IB-A6UG           TCGA-LB-A7SX 
"ST6GALNAC5 WILD-TYPE" "ST6GALNAC5 WILD-TYPE" "ST6GALNAC5 WILD-TYPE" 
          TCGA-OE-A75W 
"ST6GALNAC5 WILD-TYPE" 
D76V10, binary
                      cls
clus                    0  1
  ST6GALNAC5 MUTATED    3  0
  ST6GALNAC5 WILD-TYPE 21  9
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC5 MUTATED      3    0
  ST6GALNAC5 WILD-TYPE   21    9
    clus
vv   ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  R0                  3                   21
  R1                  0                    9
[1] 2 2
[1] FALSE
D76V11, continuous
                      vv
clus                   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ST6GALNAC5 MUTATED       0                         0     3
  ST6GALNAC5 WILD-TYPE     2                         3    25
D76V12, multiclass
                           clus
vv                          ST6GALNAC5 MUTATED ST6GALNAC5 WILD-TYPE
  ASIAN                                      0                    2
  BLACK OR AFRICAN AMERICAN                  0                    3
  WHITE                                      3                   25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = MST1 MUTATION ANALYSIS
D77V1, survival
                sevent
clus2             0  1
  MST1 MUTATED    2  2
  MST1 WILD-TYPE 16  3
  MST1 MUTATED MST1 WILD-TYPE 
             4             19 
  MST1 MUTATED MST1 WILD-TYPE 
             2              3 
$`MST1 MUTATED`
TCGA-F2-A44G TCGA-FB-A7DR TCGA-HZ-A77O TCGA-IB-7651 
         153          166           11         1989 

$`MST1 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7925 
         360          449            1          396           28          361 
TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
          13          476          851           17          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY 
        1991            8         1968          127          110          416 
TCGA-US-A776 
         844 

  MST1 MUTATED MST1 WILD-TYPE 
            11              1 
  MST1 MUTATED MST1 WILD-TYPE 
          1989           1991 
  MST1 MUTATED MST1 WILD-TYPE 
         159.5          360.0 
[1] "11.0 - 1989.0 (159.5)" "1.0 - 1991.0 (360.0)" 
[1] "hr=" "3"  
D77V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MST1 MUTATED          0         1         4         0        0
  MST1 WILD-TYPE        2         5        19         1        1
D77V3, multiclass
           clus
vv          MST1 MUTATED MST1 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            1              5
  STAGE IIB            4             19
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  MST1 MUTATED          5
  MST1 WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D77V5, binary
                cls
clus              0  1
  MST1 MUTATED    0  4
  MST1 WILD-TYPE  7 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST1 MUTATED      0    4
  MST1 WILD-TYPE    7   21
   clus
vv  MST1 MUTATED MST1 WILD-TYPE
  0            0              7
  1            4             21
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  MST1 MUTATED    3  0  2
  MST1 WILD-TYPE 16  1 11
D77V6, multiclass
    clus
vv   MST1 MUTATED MST1 WILD-TYPE
  M0            3             16
  M1            0              1
  MX            2             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                cls
clus              0  1
  MST1 MUTATED    3  2
  MST1 WILD-TYPE 11 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST1 MUTATED      3    2
  MST1 WILD-TYPE   11   17
        clus
vv       MST1 MUTATED MST1 WILD-TYPE
  FEMALE            3             11
  MALE              2             17
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MST1 MUTATED                                     4
  MST1 WILD-TYPE                                  24
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MST1 MUTATED                                       0
  MST1 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MST1 MUTATED                                                  1
  MST1 WILD-TYPE                                                1
D77V8, multiclass
                                                  clus
vv                                                 MST1 MUTATED MST1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         4             24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              3
  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"
D77V9, continuous
[1] "Remove cluster labels:" "MST1 MUTATED"          
clus
  MST1 MUTATED MST1 WILD-TYPE 
             2              9 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-H8-A6C1     TCGA-IB-7885 
"MST1 WILD-TYPE" "MST1 WILD-TYPE" "MST1 WILD-TYPE" "MST1 WILD-TYPE" 
    TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG     TCGA-LB-A7SX 
"MST1 WILD-TYPE" "MST1 WILD-TYPE" "MST1 WILD-TYPE" "MST1 WILD-TYPE" 
    TCGA-OE-A75W 
"MST1 WILD-TYPE" 
D77V10, binary
                cls
clus              0  1
  MST1 MUTATED    4  1
  MST1 WILD-TYPE 20  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST1 MUTATED      4    1
  MST1 WILD-TYPE   20    8
    clus
vv   MST1 MUTATED MST1 WILD-TYPE
  R0            4             20
  R1            1              8
[1] 2 2
[1] FALSE
D77V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MST1 MUTATED       1                         0     4
  MST1 WILD-TYPE     1                         3    24
D77V12, multiclass
                           clus
vv                          MST1 MUTATED MST1 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                4             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = GRB7 MUTATION ANALYSIS
D78V1, survival
                sevent
clus2             0  1
  GRB7 MUTATED    2  2
  GRB7 WILD-TYPE 16  3
  GRB7 MUTATED GRB7 WILD-TYPE 
             4             19 
  GRB7 MUTATED GRB7 WILD-TYPE 
             2              3 
$`GRB7 MUTATED`
TCGA-FB-A78T TCGA-IB-7651 TCGA-IB-A5SS TCGA-US-A776 
           1         1989         1991          844 

$`GRB7 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         329          300            8         1968          127          110 
TCGA-Q3-A5QY 
         416 

  GRB7 MUTATED GRB7 WILD-TYPE 
             1              8 
  GRB7 MUTATED GRB7 WILD-TYPE 
          1991           1968 
  GRB7 MUTATED GRB7 WILD-TYPE 
        1416.5          300.0 
[1] "1.0 - 1991.0 (1416.5)" "8.0 - 1968.0 (300.0)" 
[1] "hr="     "1.7e+09"
D78V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GRB7 MUTATED          0         1         3         0        0
  GRB7 WILD-TYPE        2         5        20         1        1
D78V3, multiclass
           clus
vv          GRB7 MUTATED GRB7 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            1              5
  STAGE IIB            3             20
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  GRB7 MUTATED          4
  GRB7 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D78V5, binary
                cls
clus              0  1
  GRB7 MUTATED    1  3
  GRB7 WILD-TYPE  6 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB7 MUTATED      1    3
  GRB7 WILD-TYPE    6   22
   clus
vv  GRB7 MUTATED GRB7 WILD-TYPE
  0            1              6
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  GRB7 MUTATED    3  0  1
  GRB7 WILD-TYPE 16  1 12
D78V6, multiclass
    clus
vv   GRB7 MUTATED GRB7 WILD-TYPE
  M0            3             16
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                cls
clus              0  1
  GRB7 MUTATED    3  1
  GRB7 WILD-TYPE 11 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB7 MUTATED      3    1
  GRB7 WILD-TYPE   11   18
        clus
vv       GRB7 MUTATED GRB7 WILD-TYPE
  FEMALE            3             11
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GRB7 MUTATED                                     3
  GRB7 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GRB7 MUTATED                                       0
  GRB7 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GRB7 MUTATED                                                  1
  GRB7 WILD-TYPE                                                1
D78V8, multiclass
                                                  clus
vv                                                 GRB7 MUTATED GRB7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              3
  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"
D78V9, continuous
D78V10, binary
                cls
clus              0  1
  GRB7 MUTATED    4  0
  GRB7 WILD-TYPE 20  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB7 MUTATED      4    0
  GRB7 WILD-TYPE   20    9
    clus
vv   GRB7 MUTATED GRB7 WILD-TYPE
  R0            4             20
  R1            0              9
[1] 2 2
[1] FALSE
D78V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GRB7 MUTATED       0                         0     4
  GRB7 WILD-TYPE     2                         3    24
D78V12, multiclass
                           clus
vv                          GRB7 MUTATED GRB7 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                4             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = TMC4 MUTATION ANALYSIS
D79V1, survival
                sevent
clus2             0  1
  TMC4 MUTATED    3  1
  TMC4 WILD-TYPE 15  4
  TMC4 MUTATED TMC4 WILD-TYPE 
             4             19 
  TMC4 MUTATED TMC4 WILD-TYPE 
             1              4 
$`TMC4 MUTATED`
TCGA-FB-A7DR TCGA-HZ-7925 TCGA-IB-7651 TCGA-IB-8126 
         166          361         1989           17 

$`TMC4 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449            1          396           28 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO TCGA-IB-A5SP 
          11           13          476          851          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY 
        1991            8         1968          127          110          416 
TCGA-US-A776 
         844 

  TMC4 MUTATED TMC4 WILD-TYPE 
            17              1 
  TMC4 MUTATED TMC4 WILD-TYPE 
          1989           1991 
  TMC4 MUTATED TMC4 WILD-TYPE 
         263.5          329.0 
[1] "17.0 - 1989.0 (263.5)" "1.0 - 1991.0 (329.0)" 
[1] "hr=" "1.3"
D79V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TMC4 MUTATED          0         1         2         1        0
  TMC4 WILD-TYPE        2         5        21         0        1
D79V3, multiclass
           clus
vv          TMC4 MUTATED TMC4 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            1              5
  STAGE IIB            2             21
  STAGE III            1              0
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  TMC4 MUTATED          4
  TMC4 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D79V5, binary
                cls
clus              0  1
  TMC4 MUTATED    0  3
  TMC4 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      0    3
  TMC4 WILD-TYPE    7   22
   clus
vv  TMC4 MUTATED TMC4 WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  TMC4 MUTATED    3  0  1
  TMC4 WILD-TYPE 16  1 12
D79V6, multiclass
    clus
vv   TMC4 MUTATED TMC4 WILD-TYPE
  M0            3             16
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                cls
clus              0  1
  TMC4 MUTATED    2  2
  TMC4 WILD-TYPE 12 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      2    2
  TMC4 WILD-TYPE   12   17
        clus
vv       TMC4 MUTATED TMC4 WILD-TYPE
  FEMALE            2             12
  MALE              2             17
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TMC4 MUTATED                                     3
  TMC4 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TMC4 MUTATED                                       0
  TMC4 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TMC4 MUTATED                                                  1
  TMC4 WILD-TYPE                                                1
D79V8, multiclass
                                                  clus
vv                                                 TMC4 MUTATED TMC4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              3
  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"
D79V9, continuous
D79V10, binary
                cls
clus              0  1
  TMC4 MUTATED    3  1
  TMC4 WILD-TYPE 21  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC4 MUTATED      3    1
  TMC4 WILD-TYPE   21    8
    clus
vv   TMC4 MUTATED TMC4 WILD-TYPE
  R0            3             21
  R1            1              8
[1] 2 2
[1] FALSE
D79V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMC4 MUTATED       1                         0     3
  TMC4 WILD-TYPE     1                         3    25
D79V12, multiclass
                           clus
vv                          TMC4 MUTATED TMC4 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = MED9 MUTATION ANALYSIS
D80V1, survival
                sevent
clus2             0  1
  MED9 MUTATED    1  1
  MED9 WILD-TYPE 17  4
  MED9 MUTATED MED9 WILD-TYPE 
             2             21 
  MED9 MUTATED MED9 WILD-TYPE 
             1              4 
$`MED9 MUTATED`
TCGA-IB-7651 TCGA-OE-A75W 
        1989          110 

$`MED9 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-Q3-A5QY TCGA-US-A776 
         127          416          844 

  MED9 MUTATED MED9 WILD-TYPE 
           110              1 
  MED9 MUTATED MED9 WILD-TYPE 
          1989           1991 
  MED9 MUTATED MED9 WILD-TYPE 
        1049.5          329.0 
[1] "110.0 - 1989.0 (1049.5)" "1.0 - 1991.0 (329.0)"   
[1] "Remove cluster labels:" "MED9 MUTATED"          
D80V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MED9 MUTATED          0         1         2         0        0
  MED9 WILD-TYPE        2         5        21         1        1
D80V3, multiclass
           clus
vv          MED9 MUTATED MED9 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            1              5
  STAGE IIB            2             21
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  MED9 MUTATED          3
  MED9 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D80V5, binary
                cls
clus              0  1
  MED9 MUTATED    1  2
  MED9 WILD-TYPE  6 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      1    2
  MED9 WILD-TYPE    6   23
   clus
vv  MED9 MUTATED MED9 WILD-TYPE
  0            1              6
  1            2             23
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  MED9 MUTATED    2  0  1
  MED9 WILD-TYPE 17  1 12
D80V6, multiclass
    clus
vv   MED9 MUTATED MED9 WILD-TYPE
  M0            2             17
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                cls
clus              0  1
  MED9 MUTATED    2  1
  MED9 WILD-TYPE 12 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      2    1
  MED9 WILD-TYPE   12   18
        clus
vv       MED9 MUTATED MED9 WILD-TYPE
  FEMALE            2             12
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MED9 MUTATED                                     3
  MED9 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MED9 MUTATED                                       0
  MED9 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MED9 MUTATED                                                  0
  MED9 WILD-TYPE                                                2
D80V8, multiclass
                                                  clus
vv                                                 MED9 MUTATED MED9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D80V9, continuous
[1] "Remove cluster labels:" "MED9 MUTATED"          
clus
  MED9 MUTATED MED9 WILD-TYPE 
             2              9 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG 
"MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" "MED9 WILD-TYPE" 
    TCGA-LB-A7SX 
"MED9 WILD-TYPE" 
D80V10, binary
                cls
clus              0  1
  MED9 MUTATED    3  0
  MED9 WILD-TYPE 21  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  MED9 MUTATED      3    0
  MED9 WILD-TYPE   21    9
    clus
vv   MED9 MUTATED MED9 WILD-TYPE
  R0            3             21
  R1            0              9
[1] 2 2
[1] FALSE
D80V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED9 MUTATED       0                         0     3
  MED9 WILD-TYPE     2                         3    25
D80V12, multiclass
                           clus
vv                          MED9 MUTATED MED9 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = WASF3 MUTATION ANALYSIS
D81V1, survival
                 sevent
clus2              0  1
  WASF3 MUTATED    2  0
  WASF3 WILD-TYPE 16  5
  WASF3 MUTATED WASF3 WILD-TYPE 
              2              21 
  WASF3 MUTATED WASF3 WILD-TYPE 
              0               5 
$`WASF3 MUTATED`
TCGA-IB-A5SP TCGA-OE-A75W 
         300          110 

$`WASF3 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 
          28          361           11           13         1989          476 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         851           17          329         1991            8         1968 
TCGA-LB-A7SX TCGA-Q3-A5QY TCGA-US-A776 
         127          416          844 

  WASF3 MUTATED WASF3 WILD-TYPE 
            110               1 
  WASF3 MUTATED WASF3 WILD-TYPE 
            300            1991 
  WASF3 MUTATED WASF3 WILD-TYPE 
            205             360 
[1] "110.0 - 300.0 (205.0)" "1.0 - 1991.0 (360.0)" 
[1] "Remove cluster labels:" "WASF3 MUTATED"         
D81V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  WASF3 MUTATED          0         2         1         0        0
  WASF3 WILD-TYPE        2         4        22         1        1
D81V3, multiclass
           clus
vv          WASF3 MUTATED WASF3 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             2               4
  STAGE IIB             1              22
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  WASF3 MUTATED          3
  WASF3 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D81V5, binary
                 cls
clus               0  1
  WASF3 MUTATED    2  1
  WASF3 WILD-TYPE  5 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      2    1
  WASF3 WILD-TYPE    5   24
   clus
vv  WASF3 MUTATED WASF3 WILD-TYPE
  0             2               5
  1             1              24
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  WASF3 MUTATED    2  0  1
  WASF3 WILD-TYPE 17  1 12
D81V6, multiclass
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                 cls
clus               0  1
  WASF3 MUTATED    1  2
  WASF3 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      1    2
  WASF3 WILD-TYPE   13   17
        clus
vv       WASF3 MUTATED WASF3 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WASF3 MUTATED                                     3
  WASF3 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WASF3 MUTATED                                       0
  WASF3 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WASF3 MUTATED                                                  0
  WASF3 WILD-TYPE                                                2
D81V8, multiclass
                                                  clus
vv                                                 WASF3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 WASF3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V9, continuous
[1] "Remove cluster labels:" "WASF3 MUTATED"         
clus
  WASF3 MUTATED WASF3 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"WASF3 WILD-TYPE" "WASF3 WILD-TYPE" "WASF3 WILD-TYPE" "WASF3 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS 
"WASF3 WILD-TYPE" "WASF3 WILD-TYPE" "WASF3 WILD-TYPE" "WASF3 WILD-TYPE" 
     TCGA-IB-A6UG      TCGA-LB-A7SX 
"WASF3 WILD-TYPE" "WASF3 WILD-TYPE" 
D81V10, binary
                 cls
clus               0  1
  WASF3 MUTATED    2  1
  WASF3 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WASF3 MUTATED      2    1
  WASF3 WILD-TYPE   22    8
    clus
vv   WASF3 MUTATED WASF3 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D81V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WASF3 MUTATED       0                         0     3
  WASF3 WILD-TYPE     2                         3    25
D81V12, multiclass
                           clus
vv                          WASF3 MUTATED WASF3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(82) Variable = GIT1 MUTATION ANALYSIS
D82V1, survival
                sevent
clus2             0  1
  GIT1 MUTATED    2  1
  GIT1 WILD-TYPE 16  4
  GIT1 MUTATED GIT1 WILD-TYPE 
             3             20 
  GIT1 MUTATED GIT1 WILD-TYPE 
             1              4 
$`GIT1 MUTATED`
TCGA-IB-7651 TCGA-IB-8126 TCGA-LB-A7SX 
        1989           17          127 

$`GIT1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W 
         329          300         1991            8         1968          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  GIT1 MUTATED GIT1 WILD-TYPE 
            17              1 
  GIT1 MUTATED GIT1 WILD-TYPE 
          1989           1991 
  GIT1 MUTATED GIT1 WILD-TYPE 
         127.0          344.5 
[1] "17.0 - 1989.0 (127.0)" "1.0 - 1991.0 (344.5)" 
[1] "hr=" "1"  
D82V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GIT1 MUTATED          0         0         2         1        0
  GIT1 WILD-TYPE        2         6        21         0        1
D82V3, multiclass
           clus
vv          GIT1 MUTATED GIT1 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            2             21
  STAGE III            1              0
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  GIT1 MUTATED          3
  GIT1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D82V5, binary
                cls
clus              0  1
  GIT1 MUTATED    0  3
  GIT1 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GIT1 MUTATED      0    3
  GIT1 WILD-TYPE    7   22
   clus
vv  GIT1 MUTATED GIT1 WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  GIT1 MUTATED    2  0  1
  GIT1 WILD-TYPE 17  1 12
D82V6, multiclass
    clus
vv   GIT1 MUTATED GIT1 WILD-TYPE
  M0            2             17
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                cls
clus              0  1
  GIT1 MUTATED    3  0
  GIT1 WILD-TYPE 11 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  GIT1 MUTATED      3    0
  GIT1 WILD-TYPE   11   19
        clus
vv       GIT1 MUTATED GIT1 WILD-TYPE
  FEMALE            3             11
  MALE              0             19
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GIT1 MUTATED                                     3
  GIT1 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GIT1 MUTATED                                       0
  GIT1 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GIT1 MUTATED                                                  0
  GIT1 WILD-TYPE                                                2
D82V8, multiclass
                                                  clus
vv                                                 GIT1 MUTATED GIT1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D82V9, continuous
D82V10, binary
                cls
clus              0  1
  GIT1 MUTATED    1  2
  GIT1 WILD-TYPE 23  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  GIT1 MUTATED      1    2
  GIT1 WILD-TYPE   23    7
    clus
vv   GIT1 MUTATED GIT1 WILD-TYPE
  R0            1             23
  R1            2              7
[1] 2 2
[1] FALSE
D82V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GIT1 MUTATED       0                         1     2
  GIT1 WILD-TYPE     2                         2    26
D82V12, multiclass
                           clus
vv                          GIT1 MUTATED GIT1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                2             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(83) Variable = UGP2 MUTATION ANALYSIS
D83V1, survival
                sevent
clus2             0  1
  UGP2 MUTATED    1  1
  UGP2 WILD-TYPE 17  4
  UGP2 MUTATED UGP2 WILD-TYPE 
             2             21 
  UGP2 MUTATED UGP2 WILD-TYPE 
             1              4 
$`UGP2 MUTATED`
TCGA-HZ-A77P TCGA-IB-7651 
          13         1989 

$`UGP2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28          361           11          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  UGP2 MUTATED UGP2 WILD-TYPE 
            13              1 
  UGP2 MUTATED UGP2 WILD-TYPE 
          1989           1991 
  UGP2 MUTATED UGP2 WILD-TYPE 
          1001            329 
[1] "13.0 - 1989.0 (1001.0)" "1.0 - 1991.0 (329.0)"  
[1] "Remove cluster labels:" "UGP2 MUTATED"          
D83V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  UGP2 MUTATED          0         0         4         0        0
  UGP2 WILD-TYPE        2         6        19         1        1
D83V3, multiclass
           clus
vv          UGP2 MUTATED UGP2 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            4             19
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  UGP2 MUTATED          4
  UGP2 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D83V5, binary
                cls
clus              0  1
  UGP2 MUTATED    0  4
  UGP2 WILD-TYPE  7 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      0    4
  UGP2 WILD-TYPE    7   21
   clus
vv  UGP2 MUTATED UGP2 WILD-TYPE
  0            0              7
  1            4             21
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  UGP2 MUTATED    2  0  2
  UGP2 WILD-TYPE 17  1 11
D83V6, multiclass
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  M0            2             17
  M1            0              1
  MX            2             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
                cls
clus              0  1
  UGP2 MUTATED    2  2
  UGP2 WILD-TYPE 12 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      2    2
  UGP2 WILD-TYPE   12   17
        clus
vv       UGP2 MUTATED UGP2 WILD-TYPE
  FEMALE            2             12
  MALE              2             17
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UGP2 MUTATED                                     3
  UGP2 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UGP2 MUTATED                                       1
  UGP2 WILD-TYPE                                     2
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UGP2 MUTATED                                                  0
  UGP2 WILD-TYPE                                                2
D83V8, multiclass
                                                  clus
vv                                                 UGP2 MUTATED UGP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1              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"
D83V9, continuous
[1] "Remove cluster labels:" "UGP2 MUTATED"          
clus
  UGP2 MUTATED UGP2 WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"UGP2 WILD-TYPE" "UGP2 WILD-TYPE" 
D83V10, binary
                cls
clus              0  1
  UGP2 MUTATED    4  0
  UGP2 WILD-TYPE 20  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  UGP2 MUTATED      4    0
  UGP2 WILD-TYPE   20    9
    clus
vv   UGP2 MUTATED UGP2 WILD-TYPE
  R0            4             20
  R1            0              9
[1] 2 2
[1] FALSE
D83V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UGP2 MUTATED       0                         1     3
  UGP2 WILD-TYPE     2                         2    25
D83V12, multiclass
                           clus
vv                          UGP2 MUTATED UGP2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(84) Variable = ERCC3 MUTATION ANALYSIS
D84V1, survival
                 sevent
clus2              0  1
  ERCC3 MUTATED    1  2
  ERCC3 WILD-TYPE 17  3
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              3              20 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              2               3 
$`ERCC3 MUTATED`
TCGA-F2-7273 TCGA-IB-7651 TCGA-IB-8126 
         360         1989           17 

$`ERCC3 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
         361           11           13          476          851          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  ERCC3 MUTATED ERCC3 WILD-TYPE 
             17               1 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
           1989            1991 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
          360.0           314.5 
[1] "17.0 - 1989.0 (360.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "2.8"
D84V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ERCC3 MUTATED          0         0         2         1        0
  ERCC3 WILD-TYPE        2         6        21         0        1
D84V3, multiclass
           clus
vv          ERCC3 MUTATED ERCC3 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             2              21
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  ERCC3 MUTATED          3
  ERCC3 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D84V5, binary
                 cls
clus               0  1
  ERCC3 MUTATED    0  3
  ERCC3 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED      0    3
  ERCC3 WILD-TYPE    7   22
   clus
vv  ERCC3 MUTATED ERCC3 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  ERCC3 MUTATED    3  0  0
  ERCC3 WILD-TYPE 16  1 13
D84V6, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             0              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V7, binary
                 cls
clus               0  1
  ERCC3 MUTATED    2  1
  ERCC3 WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED      2    1
  ERCC3 WILD-TYPE   12   18
        clus
vv       ERCC3 MUTATED ERCC3 WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ERCC3 MUTATED                                     3
  ERCC3 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ERCC3 MUTATED                                       0
  ERCC3 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ERCC3 MUTATED                                                  0
  ERCC3 WILD-TYPE                                                2
D84V8, multiclass
                                                  clus
vv                                                 ERCC3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 ERCC3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V9, continuous
[1] "Remove cluster labels:" "ERCC3 MUTATED"         
clus
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"ERCC3 WILD-TYPE" "ERCC3 WILD-TYPE" "ERCC3 WILD-TYPE" "ERCC3 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"ERCC3 WILD-TYPE" "ERCC3 WILD-TYPE" "ERCC3 WILD-TYPE" "ERCC3 WILD-TYPE" 
     TCGA-OE-A75W 
"ERCC3 WILD-TYPE" 
D84V10, binary
                 cls
clus               0  1
  ERCC3 MUTATED    1  2
  ERCC3 WILD-TYPE 23  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED      1    2
  ERCC3 WILD-TYPE   23    7
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  R0             1              23
  R1             2               7
[1] 2 2
[1] FALSE
D84V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERCC3 MUTATED       0                         1     2
  ERCC3 WILD-TYPE     2                         2    26
D84V12, multiclass
                           clus
vv                          ERCC3 MUTATED ERCC3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 2              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(85) Variable = HMX2 MUTATION ANALYSIS
D85V1, survival
                sevent
clus2             0  1
  HMX2 MUTATED    1  1
  HMX2 WILD-TYPE 17  4
  HMX2 MUTATED HMX2 WILD-TYPE 
             2             21 
  HMX2 MUTATED HMX2 WILD-TYPE 
             1              4 
$`HMX2 MUTATED`
TCGA-IB-7651 TCGA-IB-8126 
        1989           17 

$`HMX2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  HMX2 MUTATED HMX2 WILD-TYPE 
            17              1 
  HMX2 MUTATED HMX2 WILD-TYPE 
          1989           1991 
  HMX2 MUTATED HMX2 WILD-TYPE 
          1003            329 
[1] "17.0 - 1989.0 (1003.0)" "1.0 - 1991.0 (329.0)"  
[1] "Remove cluster labels:" "HMX2 MUTATED"          
D85V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  HMX2 MUTATED          0         0         2         1        0
  HMX2 WILD-TYPE        2         6        21         0        1
D85V3, multiclass
           clus
vv          HMX2 MUTATED HMX2 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            2             21
  STAGE III            1              0
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  HMX2 MUTATED          3
  HMX2 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D85V5, binary
                cls
clus              0  1
  HMX2 MUTATED    0  3
  HMX2 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMX2 MUTATED      0    3
  HMX2 WILD-TYPE    7   22
   clus
vv  HMX2 MUTATED HMX2 WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  HMX2 MUTATED    2  0  1
  HMX2 WILD-TYPE 17  1 12
D85V6, multiclass
    clus
vv   HMX2 MUTATED HMX2 WILD-TYPE
  M0            2             17
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V7, binary
                cls
clus              0  1
  HMX2 MUTATED    3  0
  HMX2 WILD-TYPE 11 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMX2 MUTATED      3    0
  HMX2 WILD-TYPE   11   19
        clus
vv       HMX2 MUTATED HMX2 WILD-TYPE
  FEMALE            3             11
  MALE              0             19
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HMX2 MUTATED                                     3
  HMX2 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HMX2 MUTATED                                       0
  HMX2 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HMX2 MUTATED                                                  0
  HMX2 WILD-TYPE                                                2
D85V8, multiclass
                                                  clus
vv                                                 HMX2 MUTATED HMX2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D85V9, continuous
[1] "Remove cluster labels:" "HMX2 MUTATED"          
clus
  HMX2 MUTATED HMX2 WILD-TYPE 
             2              9 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-A5SS     TCGA-IB-A6UG     TCGA-LB-A7SX 
"HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" "HMX2 WILD-TYPE" 
    TCGA-OE-A75W 
"HMX2 WILD-TYPE" 
D85V10, binary
                cls
clus              0  1
  HMX2 MUTATED    2  1
  HMX2 WILD-TYPE 22  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  HMX2 MUTATED      2    1
  HMX2 WILD-TYPE   22    8
    clus
vv   HMX2 MUTATED HMX2 WILD-TYPE
  R0            2             22
  R1            1              8
[1] 2 2
[1] FALSE
D85V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HMX2 MUTATED       0                         0     3
  HMX2 WILD-TYPE     2                         3    25
D85V12, multiclass
                           clus
vv                          HMX2 MUTATED HMX2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(86) Variable = AARS2 MUTATION ANALYSIS
D86V1, survival
                 sevent
clus2              0  1
  AARS2 MUTATED    2  1
  AARS2 WILD-TYPE 16  4
  AARS2 MUTATED AARS2 WILD-TYPE 
              3              20 
  AARS2 MUTATED AARS2 WILD-TYPE 
              1               4 
$`AARS2 MUTATED`
TCGA-H8-A6C1 TCGA-IB-7651 TCGA-IB-8126 
         396         1989           17 

$`AARS2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SO 
         361           11           13          476          851          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  AARS2 MUTATED AARS2 WILD-TYPE 
             17               1 
  AARS2 MUTATED AARS2 WILD-TYPE 
           1989            1991 
  AARS2 MUTATED AARS2 WILD-TYPE 
          396.0           314.5 
[1] "17.0 - 1989.0 (396.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.2"
D86V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  AARS2 MUTATED          0         1         2         1        0
  AARS2 WILD-TYPE        2         5        21         0        1
D86V3, multiclass
           clus
vv          AARS2 MUTATED AARS2 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             1               0
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  AARS2 MUTATED          4
  AARS2 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D86V5, binary
                 cls
clus               0  1
  AARS2 MUTATED    1  3
  AARS2 WILD-TYPE  6 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED      1    3
  AARS2 WILD-TYPE    6   22
   clus
vv  AARS2 MUTATED AARS2 WILD-TYPE
  0             1               6
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  AARS2 MUTATED    2  0  2
  AARS2 WILD-TYPE 17  1 11
D86V6, multiclass
    clus
vv   AARS2 MUTATED AARS2 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V7, binary
                 cls
clus               0  1
  AARS2 MUTATED    3  1
  AARS2 WILD-TYPE 11 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED      3    1
  AARS2 WILD-TYPE   11   18
        clus
vv       AARS2 MUTATED AARS2 WILD-TYPE
  FEMALE             3              11
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AARS2 MUTATED                                     3
  AARS2 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AARS2 MUTATED                                       1
  AARS2 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AARS2 MUTATED                                                  0
  AARS2 WILD-TYPE                                                2
D86V8, multiclass
                                                  clus
vv                                                 AARS2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 AARS2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V9, continuous
D86V10, binary
                 cls
clus               0  1
  AARS2 MUTATED    3  1
  AARS2 WILD-TYPE 21  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AARS2 MUTATED      3    1
  AARS2 WILD-TYPE   21    8
    clus
vv   AARS2 MUTATED AARS2 WILD-TYPE
  R0             3              21
  R1             1               8
[1] 2 2
[1] FALSE
D86V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AARS2 MUTATED       0                         0     4
  AARS2 WILD-TYPE     2                         3    24
D86V12, multiclass
                           clus
vv                          AARS2 MUTATED AARS2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 4              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(87) Variable = ALS2CR11 MUTATION ANALYSIS
D87V1, survival
                    sevent
clus2                 0  1
  ALS2CR11 MUTATED    2  1
  ALS2CR11 WILD-TYPE 16  4
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
                 3                 20 
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
                 1                  4 
$`ALS2CR11 MUTATED`
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
        1989          476          851 

$`ALS2CR11 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-8126 TCGA-IB-A5SO 
          28          361           11           13           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
               476                  1 
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
              1989               1991 
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
               851                233 
[1] "476.0 - 1989.0 (851.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D87V2, continuous
                    vv
clus                 STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ALS2CR11 MUTATED          0         0         3         0        0
  ALS2CR11 WILD-TYPE        2         6        20         1        1
D87V3, multiclass
           clus
vv          ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  STAGE IB                 0                  2
  STAGE IIA                0                  6
  STAGE IIB                3                 20
  STAGE III                0                  1
  STAGE IV                 0                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T2+T3+T4
  ALS2CR11 MUTATED          3
  ALS2CR11 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D87V5, binary
                    cls
clus                  0  1
  ALS2CR11 MUTATED    0  3
  ALS2CR11 WILD-TYPE  7 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ALS2CR11 MUTATED      0    3
  ALS2CR11 WILD-TYPE    7   22
   clus
vv  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  0                0                  7
  1                3                 22
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  ALS2CR11 MUTATED    3  0  0
  ALS2CR11 WILD-TYPE 16  1 13
D87V6, multiclass
    clus
vv   ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  M0                3                 16
  M1                0                  1
  MX                0                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V7, binary
                    cls
clus                  0  1
  ALS2CR11 MUTATED    3  0
  ALS2CR11 WILD-TYPE 11 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ALS2CR11 MUTATED      3    0
  ALS2CR11 WILD-TYPE   11   19
        clus
vv       ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  FEMALE                3                 11
  MALE                  0                 19
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ALS2CR11 MUTATED                                     3
  ALS2CR11 WILD-TYPE                                  25
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ALS2CR11 MUTATED                                       0
  ALS2CR11 WILD-TYPE                                     3
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ALS2CR11 MUTATED                                                  0
  ALS2CR11 WILD-TYPE                                                2
D87V8, multiclass
                                                  clus
vv                                                 ALS2CR11 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 ALS2CR11 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V9, continuous
[1] "Remove cluster labels:" "ALS2CR11 MUTATED"      
clus
  ALS2CR11 MUTATED ALS2CR11 WILD-TYPE 
                 2                  9 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-FB-A7DR 
"ALS2CR11 WILD-TYPE" "ALS2CR11 WILD-TYPE" "ALS2CR11 WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-IB-8126         TCGA-IB-A5SS 
"ALS2CR11 WILD-TYPE" "ALS2CR11 WILD-TYPE" "ALS2CR11 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-LB-A7SX         TCGA-OE-A75W 
"ALS2CR11 WILD-TYPE" "ALS2CR11 WILD-TYPE" "ALS2CR11 WILD-TYPE" 
D87V10, binary
                    cls
clus                  0  1
  ALS2CR11 MUTATED    2  1
  ALS2CR11 WILD-TYPE 22  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ALS2CR11 MUTATED      2    1
  ALS2CR11 WILD-TYPE   22    8
    clus
vv   ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  R0                2                 22
  R1                1                  8
[1] 2 2
[1] FALSE
D87V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ALS2CR11 MUTATED       1                         0     2
  ALS2CR11 WILD-TYPE     1                         3    26
D87V12, multiclass
                           clus
vv                          ALS2CR11 MUTATED ALS2CR11 WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    2                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(88) Variable = ARFGAP3 MUTATION ANALYSIS
D88V1, survival
                   sevent
clus2                0  1
  ARFGAP3 MUTATED    1  1
  ARFGAP3 WILD-TYPE 17  4
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                2                21 
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                1                 4 
$`ARFGAP3 MUTATED`
TCGA-F2-7273 TCGA-FB-A7DR 
         360          166 

$`ARFGAP3 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7925 
         153          449            1          396           28          361 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          11           13         1989          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
              166                 1 
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
              360              1991 
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
              263               329 
[1] "166.0 - 360.0 (263.0)" "1.0 - 1991.0 (329.0)" 
[1] "Remove cluster labels:" "ARFGAP3 MUTATED"       
D88V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ARFGAP3 MUTATED          0         1         2         0        0
  ARFGAP3 WILD-TYPE        2         5        21         1        1
D88V3, multiclass
           clus
vv          ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               1                 5
  STAGE IIB               2                21
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  ARFGAP3 MUTATED          3
  ARFGAP3 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D88V5, binary
                   cls
clus                 0  1
  ARFGAP3 MUTATED    0  2
  ARFGAP3 WILD-TYPE  7 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGAP3 MUTATED      0    2
  ARFGAP3 WILD-TYPE    7   23
   clus
vv  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  0               0                 7
  1               2                23
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  ARFGAP3 MUTATED    2  0  1
  ARFGAP3 WILD-TYPE 17  1 12
D88V6, multiclass
    clus
vv   ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  M0               2                17
  M1               0                 1
  MX               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V7, binary
                   cls
clus                 0  1
  ARFGAP3 MUTATED    1  2
  ARFGAP3 WILD-TYPE 13 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGAP3 MUTATED      1    2
  ARFGAP3 WILD-TYPE   13   17
        clus
vv       ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  FEMALE               1                13
  MALE                 2                17
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ARFGAP3 MUTATED                                     2
  ARFGAP3 WILD-TYPE                                  26
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ARFGAP3 MUTATED                                       0
  ARFGAP3 WILD-TYPE                                     3
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ARFGAP3 MUTATED                                                  1
  ARFGAP3 WILD-TYPE                                                1
D88V8, multiclass
                                                  clus
vv                                                 ARFGAP3 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 ARFGAP3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            3
  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"
D88V9, continuous
[1] "Remove cluster labels:" "ARFGAP3 MUTATED"       
clus
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                1                10 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-H8-A6C1        TCGA-IB-7651 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
D88V10, binary
                   cls
clus                 0  1
  ARFGAP3 MUTATED    2  1
  ARFGAP3 WILD-TYPE 22  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGAP3 MUTATED      2    1
  ARFGAP3 WILD-TYPE   22    8
    clus
vv   ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  R0               2                22
  R1               1                 8
[1] 2 2
[1] FALSE
D88V11, continuous
[1] "Remove cluster labels:" "ARFGAP3 MUTATED"       
clus
  ARFGAP3 MUTATED ARFGAP3 WILD-TYPE 
                2                30 
       TCGA-F2-A44G        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FZ-5920 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-FZ-5922        TCGA-FZ-5923        TCGA-H8-A6C1        TCGA-HZ-7918 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-HZ-7925        TCGA-HZ-8637        TCGA-HZ-A49I        TCGA-HZ-A77O 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-HZ-A77P        TCGA-IB-7651        TCGA-IB-7652        TCGA-IB-7885 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SO        TCGA-IB-A5SP        TCGA-IB-A5SQ 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-IB-A5SS        TCGA-IB-A5ST        TCGA-IB-A6UG        TCGA-LB-A7SX 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-OE-A75W        TCGA-Q3-A5QY        TCGA-US-A776        TCGA-US-A77E 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
       TCGA-US-A77G        TCGA-US-A77J 
"ARFGAP3 WILD-TYPE" "ARFGAP3 WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARFGAP3 MUTATED       1                         1     1
  ARFGAP3 WILD-TYPE     1                         2    27
D88V12, multiclass
                           clus
vv                          ARFGAP3 MUTATED ARFGAP3 WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                   1                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(89) Variable = CHGA MUTATION ANALYSIS
D89V1, survival
                sevent
clus2             0  1
  CHGA MUTATED    2  1
  CHGA WILD-TYPE 16  4
  CHGA MUTATED CHGA WILD-TYPE 
             3             20 
  CHGA MUTATED CHGA WILD-TYPE 
             1              4 
$`CHGA MUTATED`
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-IB-7651 
          28           11         1989 

$`CHGA WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7925 TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
         361           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  CHGA MUTATED CHGA WILD-TYPE 
            11              1 
  CHGA MUTATED CHGA WILD-TYPE 
          1989           1991 
  CHGA MUTATED CHGA WILD-TYPE 
          28.0          344.5 
[1] "11.0 - 1989.0 (28.0)" "1.0 - 1991.0 (344.5)"
[1] "hr=" "1"  
D89V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CHGA MUTATED          0         0         3         0        0
  CHGA WILD-TYPE        2         6        20         1        1
D89V3, multiclass
           clus
vv          CHGA MUTATED CHGA WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            3             20
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  CHGA MUTATED          3
  CHGA WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D89V5, binary
                cls
clus              0  1
  CHGA MUTATED    0  3
  CHGA WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGA MUTATED      0    3
  CHGA WILD-TYPE    7   22
   clus
vv  CHGA MUTATED CHGA WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  CHGA MUTATED    2  0  1
  CHGA WILD-TYPE 17  1 12
D89V6, multiclass
    clus
vv   CHGA MUTATED CHGA WILD-TYPE
  M0            2             17
  M1            0              1
  MX            1             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V7, binary
                cls
clus              0  1
  CHGA MUTATED    2  1
  CHGA WILD-TYPE 12 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGA MUTATED      2    1
  CHGA WILD-TYPE   12   18
        clus
vv       CHGA MUTATED CHGA WILD-TYPE
  FEMALE            2             12
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CHGA MUTATED                                     3
  CHGA WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CHGA MUTATED                                       0
  CHGA WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CHGA MUTATED                                                  0
  CHGA WILD-TYPE                                                2
D89V8, multiclass
                                                  clus
vv                                                 CHGA MUTATED CHGA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D89V9, continuous
[1] "Remove cluster labels:" "CHGA MUTATED"          
clus
  CHGA MUTATED CHGA WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"CHGA WILD-TYPE" "CHGA WILD-TYPE" "CHGA WILD-TYPE" "CHGA WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG 
"CHGA WILD-TYPE" "CHGA WILD-TYPE" "CHGA WILD-TYPE" "CHGA WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"CHGA WILD-TYPE" "CHGA WILD-TYPE" 
D89V10, binary
                cls
clus              0  1
  CHGA MUTATED    3  0
  CHGA WILD-TYPE 21  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHGA MUTATED      3    0
  CHGA WILD-TYPE   21    9
    clus
vv   CHGA MUTATED CHGA WILD-TYPE
  R0            3             21
  R1            0              9
[1] 2 2
[1] FALSE
D89V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHGA MUTATED       0                         0     3
  CHGA WILD-TYPE     2                         3    25
D89V12, multiclass
                           clus
vv                          CHGA MUTATED CHGA WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(90) Variable = FAM63B MUTATION ANALYSIS
D90V1, survival
                  sevent
clus2               0  1
  FAM63B MUTATED    0  2
  FAM63B WILD-TYPE 18  3
  FAM63B MUTATED FAM63B WILD-TYPE 
               2               21 
  FAM63B MUTATED FAM63B WILD-TYPE 
               2                3 
$`FAM63B MUTATED`
TCGA-IB-7651 TCGA-IB-A6UG 
        1989         1968 

$`FAM63B WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-LB-A7SX 
          17          329          300         1991            8          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  FAM63B MUTATED FAM63B WILD-TYPE 
            1968                1 
  FAM63B MUTATED FAM63B WILD-TYPE 
            1989             1991 
  FAM63B MUTATED FAM63B WILD-TYPE 
          1978.5            300.0 
[1] "1968.0 - 1989.0 (1978.5)" "1.0 - 1991.0 (300.0)"    
[1] "Remove cluster labels:" "FAM63B MUTATED"        
D90V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FAM63B MUTATED          0         0         3         0        0
  FAM63B WILD-TYPE        2         6        20         1        1
D90V3, multiclass
           clus
vv          FAM63B MUTATED FAM63B WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              0                6
  STAGE IIB              3               20
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  FAM63B MUTATED          3
  FAM63B WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D90V5, binary
                  cls
clus                0  1
  FAM63B MUTATED    0  3
  FAM63B WILD-TYPE  7 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM63B MUTATED      0    3
  FAM63B WILD-TYPE    7   22
   clus
vv  FAM63B MUTATED FAM63B WILD-TYPE
  0              0                7
  1              3               22
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  FAM63B MUTATED    2  0  1
  FAM63B WILD-TYPE 17  1 12
D90V6, multiclass
    clus
vv   FAM63B MUTATED FAM63B WILD-TYPE
  M0              2               17
  M1              0                1
  MX              1               12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V7, binary
                  cls
clus                0  1
  FAM63B MUTATED    2  1
  FAM63B WILD-TYPE 12 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM63B MUTATED      2    1
  FAM63B WILD-TYPE   12   18
        clus
vv       FAM63B MUTATED FAM63B WILD-TYPE
  FEMALE              2               12
  MALE                1               18
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FAM63B MUTATED                                     3
  FAM63B WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FAM63B MUTATED                                       0
  FAM63B WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FAM63B MUTATED                                                  0
  FAM63B WILD-TYPE                                                2
D90V8, multiclass
                                                  clus
vv                                                 FAM63B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 FAM63B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V9, continuous
[1] "Remove cluster labels:" "FAM63B MUTATED"        
clus
  FAM63B MUTATED FAM63B WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-H8-A6C1 
"FAM63B WILD-TYPE" "FAM63B WILD-TYPE" "FAM63B WILD-TYPE" "FAM63B WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A5SS       TCGA-LB-A7SX 
"FAM63B WILD-TYPE" "FAM63B WILD-TYPE" "FAM63B WILD-TYPE" "FAM63B WILD-TYPE" 
      TCGA-OE-A75W 
"FAM63B WILD-TYPE" 
D90V10, binary
                  cls
clus                0  1
  FAM63B MUTATED    2  1
  FAM63B WILD-TYPE 22  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM63B MUTATED      2    1
  FAM63B WILD-TYPE   22    8
    clus
vv   FAM63B MUTATED FAM63B WILD-TYPE
  R0              2               22
  R1              1                8
[1] 2 2
[1] FALSE
D90V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM63B MUTATED       0                         0     3
  FAM63B WILD-TYPE     2                         3    25
D90V12, multiclass
                           clus
vv                          FAM63B MUTATED FAM63B WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(91) Variable = VPS36 MUTATION ANALYSIS
D91V1, survival
                 sevent
clus2              0  1
  VPS36 MUTATED    1  2
  VPS36 WILD-TYPE 17  3
  VPS36 MUTATED VPS36 WILD-TYPE 
              3              20 
  VPS36 MUTATED VPS36 WILD-TYPE 
              2               3 
$`VPS36 MUTATED`
TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-A5SS 
          13         1989         1991 

$`VPS36 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28          361           11          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         329          300            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  VPS36 MUTATED VPS36 WILD-TYPE 
             13               1 
  VPS36 MUTATED VPS36 WILD-TYPE 
           1991            1968 
  VPS36 MUTATED VPS36 WILD-TYPE 
         1989.0           314.5 
[1] "13.0 - 1991.0 (1989.0)" "1.0 - 1968.0 (314.5)"  
[1] "hr="     "1.8e+09"
D91V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  VPS36 MUTATED          0         0         3         0        0
  VPS36 WILD-TYPE        2         6        20         1        1
D91V3, multiclass
           clus
vv          VPS36 MUTATED VPS36 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  VPS36 MUTATED          3
  VPS36 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D91V5, binary
                 cls
clus               0  1
  VPS36 MUTATED    0  3
  VPS36 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS36 MUTATED      0    3
  VPS36 WILD-TYPE    7   22
   clus
vv  VPS36 MUTATED VPS36 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  VPS36 MUTATED    2  0  1
  VPS36 WILD-TYPE 17  1 12
D91V6, multiclass
    clus
vv   VPS36 MUTATED VPS36 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V7, binary
                 cls
clus               0  1
  VPS36 MUTATED    2  1
  VPS36 WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS36 MUTATED      2    1
  VPS36 WILD-TYPE   12   18
        clus
vv       VPS36 MUTATED VPS36 WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  VPS36 MUTATED                                     2
  VPS36 WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  VPS36 MUTATED                                       1
  VPS36 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  VPS36 MUTATED                                                  0
  VPS36 WILD-TYPE                                                2
D91V8, multiclass
                                                  clus
vv                                                 VPS36 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 VPS36 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V9, continuous
[1] "Remove cluster labels:" "VPS36 MUTATED"         
clus
  VPS36 MUTATED VPS36 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"VPS36 WILD-TYPE" "VPS36 WILD-TYPE" "VPS36 WILD-TYPE" "VPS36 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UG      TCGA-LB-A7SX 
"VPS36 WILD-TYPE" "VPS36 WILD-TYPE" "VPS36 WILD-TYPE" "VPS36 WILD-TYPE" 
     TCGA-OE-A75W 
"VPS36 WILD-TYPE" 
D91V10, binary
                 cls
clus               0  1
  VPS36 MUTATED    3  0
  VPS36 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS36 MUTATED      3    0
  VPS36 WILD-TYPE   21    9
    clus
vv   VPS36 MUTATED VPS36 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D91V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VPS36 MUTATED       0                         0     3
  VPS36 WILD-TYPE     2                         3    25
D91V12, multiclass
                           clus
vv                          VPS36 MUTATED VPS36 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(92) Variable = MAP3K7 MUTATION ANALYSIS
D92V1, survival
                  sevent
clus2               0  1
  MAP3K7 MUTATED    1  1
  MAP3K7 WILD-TYPE 17  4
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               2               21 
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               1                4 
$`MAP3K7 MUTATED`
TCGA-IB-7651 TCGA-IB-8126 
        1989           17 

$`MAP3K7 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
              17                1 
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
            1989             1991 
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
            1003              329 
[1] "17.0 - 1989.0 (1003.0)" "1.0 - 1991.0 (329.0)"  
[1] "Remove cluster labels:" "MAP3K7 MUTATED"        
D92V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MAP3K7 MUTATED          0         0         2         1        0
  MAP3K7 WILD-TYPE        2         6        21         0        1
D92V3, multiclass
           clus
vv          MAP3K7 MUTATED MAP3K7 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              0                6
  STAGE IIB              2               21
  STAGE III              1                0
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  MAP3K7 MUTATED          3
  MAP3K7 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D92V5, binary
                  cls
clus                0  1
  MAP3K7 MUTATED    0  3
  MAP3K7 WILD-TYPE  7 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K7 MUTATED      0    3
  MAP3K7 WILD-TYPE    7   22
   clus
vv  MAP3K7 MUTATED MAP3K7 WILD-TYPE
  0              0                7
  1              3               22
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  MAP3K7 MUTATED    2  0  1
  MAP3K7 WILD-TYPE 17  1 12
D92V6, multiclass
    clus
vv   MAP3K7 MUTATED MAP3K7 WILD-TYPE
  M0              2               17
  M1              0                1
  MX              1               12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V7, binary
                  cls
clus                0  1
  MAP3K7 MUTATED    3  0
  MAP3K7 WILD-TYPE 11 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K7 MUTATED      3    0
  MAP3K7 WILD-TYPE   11   19
        clus
vv       MAP3K7 MUTATED MAP3K7 WILD-TYPE
  FEMALE              3               11
  MALE                0               19
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MAP3K7 MUTATED                                     3
  MAP3K7 WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MAP3K7 MUTATED                                       0
  MAP3K7 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MAP3K7 MUTATED                                                  0
  MAP3K7 WILD-TYPE                                                2
D92V8, multiclass
                                                  clus
vv                                                 MAP3K7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 MAP3K7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V9, continuous
[1] "Remove cluster labels:" "MAP3K7 MUTATED"        
clus
  MAP3K7 MUTATED MAP3K7 WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-H8-A6C1 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-LB-A7SX 
"MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" "MAP3K7 WILD-TYPE" 
      TCGA-OE-A75W 
"MAP3K7 WILD-TYPE" 
D92V10, binary
                  cls
clus                0  1
  MAP3K7 MUTATED    2  1
  MAP3K7 WILD-TYPE 22  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K7 MUTATED      2    1
  MAP3K7 WILD-TYPE   22    8
    clus
vv   MAP3K7 MUTATED MAP3K7 WILD-TYPE
  R0              2               22
  R1              1                8
[1] 2 2
[1] FALSE
D92V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MAP3K7 MUTATED       0                         0     3
  MAP3K7 WILD-TYPE     2                         3    25
D92V12, multiclass
                           clus
vv                          MAP3K7 MUTATED MAP3K7 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(93) Variable = OTX1 MUTATION ANALYSIS
D93V1, survival
                sevent
clus2             0  1
  OTX1 MUTATED    2  1
  OTX1 WILD-TYPE 16  4
  OTX1 MUTATED OTX1 WILD-TYPE 
             3             20 
  OTX1 MUTATED OTX1 WILD-TYPE 
             1              4 
$`OTX1 MUTATED`
TCGA-FB-A78T TCGA-IB-7651 TCGA-LB-A7SX 
           1         1989          127 

$`OTX1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W 
         329          300         1991            8         1968          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  OTX1 MUTATED OTX1 WILD-TYPE 
             1              8 
  OTX1 MUTATED OTX1 WILD-TYPE 
          1989           1991 
  OTX1 MUTATED OTX1 WILD-TYPE 
         127.0          344.5 
[1] "1.0 - 1989.0 (127.0)" "8.0 - 1991.0 (344.5)"
[1] "hr=" "1"  
D93V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  OTX1 MUTATED          0         0         4         0        0
  OTX1 WILD-TYPE        2         6        19         1        1
D93V3, multiclass
           clus
vv          OTX1 MUTATED OTX1 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            4             19
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  OTX1 MUTATED          4
  OTX1 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D93V5, binary
                cls
clus              0  1
  OTX1 MUTATED    0  4
  OTX1 WILD-TYPE  7 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX1 MUTATED      0    4
  OTX1 WILD-TYPE    7   21
   clus
vv  OTX1 MUTATED OTX1 WILD-TYPE
  0            0              7
  1            4             21
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  OTX1 MUTATED    2  0  2
  OTX1 WILD-TYPE 17  1 11
D93V6, multiclass
    clus
vv   OTX1 MUTATED OTX1 WILD-TYPE
  M0            2             17
  M1            0              1
  MX            2             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V7, binary
                cls
clus              0  1
  OTX1 MUTATED    3  1
  OTX1 WILD-TYPE 11 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX1 MUTATED      3    1
  OTX1 WILD-TYPE   11   18
        clus
vv       OTX1 MUTATED OTX1 WILD-TYPE
  FEMALE            3             11
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  OTX1 MUTATED                                     3
  OTX1 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  OTX1 MUTATED                                       1
  OTX1 WILD-TYPE                                     2
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  OTX1 MUTATED                                                  0
  OTX1 WILD-TYPE                                                2
D93V8, multiclass
                                                  clus
vv                                                 OTX1 MUTATED OTX1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1              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"
D93V9, continuous
D93V10, binary
                cls
clus              0  1
  OTX1 MUTATED    2  2
  OTX1 WILD-TYPE 22  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX1 MUTATED      2    2
  OTX1 WILD-TYPE   22    7
    clus
vv   OTX1 MUTATED OTX1 WILD-TYPE
  R0            2             22
  R1            2              7
[1] 2 2
[1] FALSE
D93V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTX1 MUTATED       0                         1     3
  OTX1 WILD-TYPE     2                         2    25
D93V12, multiclass
                           clus
vv                          OTX1 MUTATED OTX1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(94) Variable = NFAT5 MUTATION ANALYSIS
D94V1, survival
                 sevent
clus2              0  1
  NFAT5 MUTATED    1  2
  NFAT5 WILD-TYPE 17  3
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              3              20 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              2               3 
$`NFAT5 MUTATED`
TCGA-F2-A44G TCGA-IB-7651 TCGA-IB-7885 
         153         1989          851 

$`NFAT5 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO 
         361           11           13          476           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  NFAT5 MUTATED NFAT5 WILD-TYPE 
            153               1 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
           1989            1991 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
          851.0           314.5 
[1] "153.0 - 1989.0 (851.0)" "1.0 - 1991.0 (314.5)"  
[1] "hr=" "2.5"
D94V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NFAT5 MUTATED          0         0         3         0        0
  NFAT5 WILD-TYPE        2         6        20         1        1
D94V3, multiclass
           clus
vv          NFAT5 MUTATED NFAT5 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  NFAT5 MUTATED          3
  NFAT5 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D94V5, binary
                 cls
clus               0  1
  NFAT5 MUTATED    0  3
  NFAT5 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      0    3
  NFAT5 WILD-TYPE    7   22
   clus
vv  NFAT5 MUTATED NFAT5 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  NFAT5 MUTATED    3  0  0
  NFAT5 WILD-TYPE 16  1 13
D94V6, multiclass
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             0              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V7, binary
                 cls
clus               0  1
  NFAT5 MUTATED    3  0
  NFAT5 WILD-TYPE 11 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      3    0
  NFAT5 WILD-TYPE   11   19
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  FEMALE             3              11
  MALE               0              19
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NFAT5 MUTATED                                     3
  NFAT5 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NFAT5 MUTATED                                       0
  NFAT5 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NFAT5 MUTATED                                                  0
  NFAT5 WILD-TYPE                                                2
D94V8, multiclass
                                                  clus
vv                                                 NFAT5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NFAT5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V9, continuous
[1] "Remove cluster labels:" "NFAT5 MUTATED"         
clus
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" "NFAT5 WILD-TYPE" 
     TCGA-OE-A75W 
"NFAT5 WILD-TYPE" 
D94V10, binary
                 cls
clus               0  1
  NFAT5 MUTATED    2  1
  NFAT5 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      2    1
  NFAT5 WILD-TYPE   22    8
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D94V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFAT5 MUTATED       0                         0     3
  NFAT5 WILD-TYPE     2                         3    25
D94V12, multiclass
                           clus
vv                          NFAT5 MUTATED NFAT5 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(95) Variable = WHSC1L1 MUTATION ANALYSIS
D95V1, survival
                   sevent
clus2                0  1
  WHSC1L1 MUTATED    2  0
  WHSC1L1 WILD-TYPE 16  5
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                2                21 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                0                 5 
$`WHSC1L1 MUTATED`
TCGA-IB-7652 TCGA-IB-8126 
         476           17 

$`WHSC1L1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7885 
          28          361           11           13         1989          851 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
               17                 1 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
              476              1991 
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
            246.5             329.0 
[1] "17.0 - 476.0 (246.5)" "1.0 - 1991.0 (329.0)"
[1] "Remove cluster labels:" "WHSC1L1 MUTATED"       
D95V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  WHSC1L1 MUTATED          0         0         2         1        0
  WHSC1L1 WILD-TYPE        2         6        21         0        1
D95V3, multiclass
           clus
vv          WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               0                 6
  STAGE IIB               2                21
  STAGE III               1                 0
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  WHSC1L1 MUTATED          3
  WHSC1L1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D95V5, binary
                   cls
clus                 0  1
  WHSC1L1 MUTATED    0  3
  WHSC1L1 WILD-TYPE  7 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      0    3
  WHSC1L1 WILD-TYPE    7   22
   clus
vv  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  0               0                 7
  1               3                22
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  WHSC1L1 MUTATED    2  0  1
  WHSC1L1 WILD-TYPE 17  1 12
D95V6, multiclass
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  M0               2                17
  M1               0                 1
  MX               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V7, binary
                   cls
clus                 0  1
  WHSC1L1 MUTATED    2  1
  WHSC1L1 WILD-TYPE 12 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      2    1
  WHSC1L1 WILD-TYPE   12   18
        clus
vv       WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  FEMALE               2                12
  MALE                 1                18
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  WHSC1L1 MUTATED                                     3
  WHSC1L1 WILD-TYPE                                  25
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  WHSC1L1 MUTATED                                       0
  WHSC1L1 WILD-TYPE                                     3
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  WHSC1L1 MUTATED                                                  0
  WHSC1L1 WILD-TYPE                                                2
D95V8, multiclass
                                                  clus
vv                                                 WHSC1L1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 WHSC1L1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V9, continuous
[1] "Remove cluster labels:" "WHSC1L1 MUTATED"       
clus
  WHSC1L1 MUTATED WHSC1L1 WILD-TYPE 
                1                10 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-H8-A6C1 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-IB-7651        TCGA-IB-7885        TCGA-IB-A5SS        TCGA-IB-A6UG 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W 
"WHSC1L1 WILD-TYPE" "WHSC1L1 WILD-TYPE" 
D95V10, binary
                   cls
clus                 0  1
  WHSC1L1 MUTATED    0  3
  WHSC1L1 WILD-TYPE 24  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WHSC1L1 MUTATED      0    3
  WHSC1L1 WILD-TYPE   24    6
    clus
vv   WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  R0               0                24
  R1               3                 6
[1] 2 2
[1] FALSE
D95V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  WHSC1L1 MUTATED       1                         0     2
  WHSC1L1 WILD-TYPE     1                         3    26
D95V12, multiclass
                           clus
vv                          WHSC1L1 MUTATED WHSC1L1 WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   2                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(96) Variable = KIAA1211 MUTATION ANALYSIS
D96V1, survival
                    sevent
clus2                 0  1
  KIAA1211 MUTATED    1  1
  KIAA1211 WILD-TYPE 17  4
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 2                 21 
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 1                  4 
$`KIAA1211 MUTATED`
TCGA-FB-A7DR TCGA-IB-7651 
         166         1989 

$`KIAA1211 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449            1          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
               166                  1 
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
              1989               1991 
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
            1077.5              329.0 
[1] "166.0 - 1989.0 (1077.5)" "1.0 - 1991.0 (329.0)"   
[1] "Remove cluster labels:" "KIAA1211 MUTATED"      
D96V2, continuous
                    vv
clus                 STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  KIAA1211 MUTATED          0         1         2         0        0
  KIAA1211 WILD-TYPE        2         5        21         1        1
D96V3, multiclass
           clus
vv          KIAA1211 MUTATED KIAA1211 WILD-TYPE
  STAGE IB                 0                  2
  STAGE IIA                1                  5
  STAGE IIB                2                 21
  STAGE III                0                  1
  STAGE IV                 0                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T2+T3+T4
  KIAA1211 MUTATED          3
  KIAA1211 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D96V5, binary
                    cls
clus                  0  1
  KIAA1211 MUTATED    0  2
  KIAA1211 WILD-TYPE  7 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1211 MUTATED      0    2
  KIAA1211 WILD-TYPE    7   23
   clus
vv  KIAA1211 MUTATED KIAA1211 WILD-TYPE
  0                0                  7
  1                2                 23
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  KIAA1211 MUTATED    2  0  1
  KIAA1211 WILD-TYPE 17  1 12
D96V6, multiclass
    clus
vv   KIAA1211 MUTATED KIAA1211 WILD-TYPE
  M0                2                 17
  M1                0                  1
  MX                1                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V7, binary
                    cls
clus                  0  1
  KIAA1211 MUTATED    2  1
  KIAA1211 WILD-TYPE 12 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1211 MUTATED      2    1
  KIAA1211 WILD-TYPE   12   18
        clus
vv       KIAA1211 MUTATED KIAA1211 WILD-TYPE
  FEMALE                2                 12
  MALE                  1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  KIAA1211 MUTATED                                     2
  KIAA1211 WILD-TYPE                                  26
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  KIAA1211 MUTATED                                       0
  KIAA1211 WILD-TYPE                                     3
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  KIAA1211 MUTATED                                                  1
  KIAA1211 WILD-TYPE                                                1
D96V8, multiclass
                                                  clus
vv                                                 KIAA1211 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 KIAA1211 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             3
  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"
D96V9, continuous
[1] "Remove cluster labels:" "KIAA1211 MUTATED"      
clus
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 2                  9 
        TCGA-FB-A5VM         TCGA-FB-A78T         TCGA-H8-A6C1 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-8126         TCGA-IB-A5SS 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-LB-A7SX         TCGA-OE-A75W 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
D96V10, binary
                    cls
clus                  0  1
  KIAA1211 MUTATED    3  0
  KIAA1211 WILD-TYPE 21  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1211 MUTATED      3    0
  KIAA1211 WILD-TYPE   21    9
    clus
vv   KIAA1211 MUTATED KIAA1211 WILD-TYPE
  R0                3                 21
  R1                0                  9
[1] 2 2
[1] FALSE
D96V11, continuous
[1] "Remove cluster labels:" "KIAA1211 MUTATED"      
clus
  KIAA1211 MUTATED KIAA1211 WILD-TYPE 
                 2                 30 
        TCGA-F2-7273         TCGA-F2-A44G         TCGA-FB-A5VM 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FZ-5920         TCGA-FZ-5922 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-FZ-5923         TCGA-H8-A6C1         TCGA-HZ-7918 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-HZ-7925         TCGA-HZ-A49I         TCGA-HZ-A77O 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-HZ-A77P         TCGA-IB-7652         TCGA-IB-7885 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-A5SO         TCGA-IB-A5SP 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-A5SQ         TCGA-IB-A5SS         TCGA-IB-A5ST 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-LB-A7SX         TCGA-OE-A75W 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-Q3-A5QY         TCGA-US-A776         TCGA-US-A779 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
        TCGA-US-A77E         TCGA-US-A77G         TCGA-US-A77J 
"KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" "KIAA1211 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1211 MUTATED       1                         0     2
  KIAA1211 WILD-TYPE     1                         3    26
D96V12, multiclass
                           clus
vv                          KIAA1211 MUTATED KIAA1211 WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    2                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(97) Variable = PPIG MUTATION ANALYSIS
D97V1, survival
                sevent
clus2             0  1
  PPIG MUTATED    0  2
  PPIG WILD-TYPE 18  3
  PPIG MUTATED PPIG WILD-TYPE 
             2             21 
  PPIG MUTATED PPIG WILD-TYPE 
             2              3 
$`PPIG MUTATED`
TCGA-F2-7273 TCGA-IB-7651 
         360         1989 

$`PPIG WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  PPIG MUTATED PPIG WILD-TYPE 
           360              1 
  PPIG MUTATED PPIG WILD-TYPE 
          1989           1991 
  PPIG MUTATED PPIG WILD-TYPE 
        1174.5          300.0 
[1] "360.0 - 1989.0 (1174.5)" "1.0 - 1991.0 (300.0)"   
[1] "Remove cluster labels:" "PPIG MUTATED"          
D97V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PPIG MUTATED          0         1         2         0        0
  PPIG WILD-TYPE        2         5        21         1        1
D97V3, multiclass
           clus
vv          PPIG MUTATED PPIG WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            1              5
  STAGE IIB            2             21
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  PPIG MUTATED          3
  PPIG WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D97V5, binary
                cls
clus              0  1
  PPIG MUTATED    1  2
  PPIG WILD-TYPE  6 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      1    2
  PPIG WILD-TYPE    6   23
   clus
vv  PPIG MUTATED PPIG WILD-TYPE
  0            1              6
  1            2             23
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  PPIG MUTATED    3  0  0
  PPIG WILD-TYPE 16  1 13
D97V6, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  M0            3             16
  M1            0              1
  MX            0             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V7, binary
                cls
clus              0  1
  PPIG MUTATED    1  2
  PPIG WILD-TYPE 13 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      1    2
  PPIG WILD-TYPE   13   17
        clus
vv       PPIG MUTATED PPIG WILD-TYPE
  FEMALE            1             13
  MALE              2             17
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PPIG MUTATED                                     3
  PPIG WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PPIG MUTATED                                       0
  PPIG WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PPIG MUTATED                                                  0
  PPIG WILD-TYPE                                                2
D97V8, multiclass
                                                  clus
vv                                                 PPIG MUTATED PPIG WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D97V9, continuous
[1] "Remove cluster labels:" "PPIG MUTATED"          
clus
  PPIG MUTATED PPIG WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" "PPIG WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"PPIG WILD-TYPE" "PPIG WILD-TYPE" 
D97V10, binary
                cls
clus              0  1
  PPIG MUTATED    2  1
  PPIG WILD-TYPE 22  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      2    1
  PPIG WILD-TYPE   22    8
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  R0            2             22
  R1            1              8
[1] 2 2
[1] FALSE
D97V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PPIG MUTATED       0                         1     2
  PPIG WILD-TYPE     2                         2    26
D97V12, multiclass
                           clus
vv                          PPIG MUTATED PPIG WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                2             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(98) Variable = SLITRK5 MUTATION ANALYSIS
D98V1, survival
                   sevent
clus2                0  1
  SLITRK5 MUTATED    1  2
  SLITRK5 WILD-TYPE 17  3
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
                3                20 
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
                2                 3 
$`SLITRK5 MUTATED`
TCGA-F2-A44G TCGA-HZ-A77P TCGA-IB-7651 
         153           13         1989 

$`SLITRK5 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
         361           11          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
               13                 1 
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
             1989              1991 
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
            153.0             344.5 
[1] "13.0 - 1989.0 (153.0)" "1.0 - 1991.0 (344.5)" 
[1] "hr=" "3.4"
D98V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SLITRK5 MUTATED          0         0         3         0        0
  SLITRK5 WILD-TYPE        2         6        20         1        1
D98V3, multiclass
           clus
vv          SLITRK5 MUTATED SLITRK5 WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               0                 6
  STAGE IIB               3                20
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  SLITRK5 MUTATED          3
  SLITRK5 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D98V5, binary
                   cls
clus                 0  1
  SLITRK5 MUTATED    0  3
  SLITRK5 WILD-TYPE  7 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK5 MUTATED      0    3
  SLITRK5 WILD-TYPE    7   22
   clus
vv  SLITRK5 MUTATED SLITRK5 WILD-TYPE
  0               0                 7
  1               3                22
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  SLITRK5 MUTATED    2  0  1
  SLITRK5 WILD-TYPE 17  1 12
D98V6, multiclass
    clus
vv   SLITRK5 MUTATED SLITRK5 WILD-TYPE
  M0               2                17
  M1               0                 1
  MX               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V7, binary
                   cls
clus                 0  1
  SLITRK5 MUTATED    2  1
  SLITRK5 WILD-TYPE 12 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK5 MUTATED      2    1
  SLITRK5 WILD-TYPE   12   18
        clus
vv       SLITRK5 MUTATED SLITRK5 WILD-TYPE
  FEMALE               2                12
  MALE                 1                18
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SLITRK5 MUTATED                                     2
  SLITRK5 WILD-TYPE                                  26
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SLITRK5 MUTATED                                       1
  SLITRK5 WILD-TYPE                                     2
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SLITRK5 MUTATED                                                  0
  SLITRK5 WILD-TYPE                                                2
D98V8, multiclass
                                                  clus
vv                                                 SLITRK5 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 SLITRK5 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V9, continuous
[1] "Remove cluster labels:" "SLITRK5 MUTATED"       
clus
  SLITRK5 MUTATED SLITRK5 WILD-TYPE 
                1                10 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-H8-A6C1 
"SLITRK5 WILD-TYPE" "SLITRK5 WILD-TYPE" "SLITRK5 WILD-TYPE" "SLITRK5 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG 
"SLITRK5 WILD-TYPE" "SLITRK5 WILD-TYPE" "SLITRK5 WILD-TYPE" "SLITRK5 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W 
"SLITRK5 WILD-TYPE" "SLITRK5 WILD-TYPE" 
D98V10, binary
                   cls
clus                 0  1
  SLITRK5 MUTATED    2  1
  SLITRK5 WILD-TYPE 22  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK5 MUTATED      2    1
  SLITRK5 WILD-TYPE   22    8
    clus
vv   SLITRK5 MUTATED SLITRK5 WILD-TYPE
  R0               2                22
  R1               1                 8
[1] 2 2
[1] FALSE
D98V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLITRK5 MUTATED       0                         0     3
  SLITRK5 WILD-TYPE     2                         3    25
D98V12, multiclass
                           clus
vv                          SLITRK5 MUTATED SLITRK5 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   3                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(99) Variable = MBD3 MUTATION ANALYSIS
D99V1, survival
                sevent
clus2             0  1
  MBD3 MUTATED    1  2
  MBD3 WILD-TYPE 17  3
  MBD3 MUTATED MBD3 WILD-TYPE 
             3             20 
  MBD3 MUTATED MBD3 WILD-TYPE 
             2              3 
$`MBD3 MUTATED`
TCGA-F2-7273 TCGA-IB-7651 TCGA-IB-A5SO 
         360         1989          329 

$`MBD3 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  MBD3 MUTATED MBD3 WILD-TYPE 
           329              1 
  MBD3 MUTATED MBD3 WILD-TYPE 
          1989           1991 
  MBD3 MUTATED MBD3 WILD-TYPE 
           360            233 
[1] "329.0 - 1989.0 (360.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "2.5"
D99V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MBD3 MUTATED          0         0         3         0        0
  MBD3 WILD-TYPE        2         6        20         1        1
D99V3, multiclass
           clus
vv          MBD3 MUTATED MBD3 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            3             20
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  MBD3 MUTATED          3
  MBD3 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D99V5, binary
                cls
clus              0  1
  MBD3 MUTATED    0  3
  MBD3 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      0    3
  MBD3 WILD-TYPE    7   22
   clus
vv  MBD3 MUTATED MBD3 WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  MBD3 MUTATED    3  0  0
  MBD3 WILD-TYPE 16  1 13
D99V6, multiclass
    clus
vv   MBD3 MUTATED MBD3 WILD-TYPE
  M0            3             16
  M1            0              1
  MX            0             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V7, binary
                cls
clus              0  1
  MBD3 MUTATED    1  2
  MBD3 WILD-TYPE 13 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      1    2
  MBD3 WILD-TYPE   13   17
        clus
vv       MBD3 MUTATED MBD3 WILD-TYPE
  FEMALE            1             13
  MALE              2             17
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MBD3 MUTATED                                     3
  MBD3 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MBD3 MUTATED                                       0
  MBD3 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MBD3 MUTATED                                                  0
  MBD3 WILD-TYPE                                                2
D99V8, multiclass
                                                  clus
vv                                                 MBD3 MUTATED MBD3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D99V9, continuous
[1] "Remove cluster labels:" "MBD3 MUTATED"          
clus
  MBD3 MUTATED MBD3 WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"MBD3 WILD-TYPE" "MBD3 WILD-TYPE" 
D99V10, binary
                cls
clus              0  1
  MBD3 MUTATED    2  1
  MBD3 WILD-TYPE 22  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD3 MUTATED      2    1
  MBD3 WILD-TYPE   22    8
    clus
vv   MBD3 MUTATED MBD3 WILD-TYPE
  R0            2             22
  R1            1              8
[1] 2 2
[1] FALSE
D99V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MBD3 MUTATED       0                         1     2
  MBD3 WILD-TYPE     2                         2    26
D99V12, multiclass
                           clus
vv                          MBD3 MUTATED MBD3 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              2
  WHITE                                2             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(100) Variable = FOXP2 MUTATION ANALYSIS
D100V1, survival
                 sevent
clus2              0  1
  FOXP2 MUTATED    1  2
  FOXP2 WILD-TYPE 17  3
  FOXP2 MUTATED FOXP2 WILD-TYPE 
              3              20 
  FOXP2 MUTATED FOXP2 WILD-TYPE 
              2               3 
$`FOXP2 MUTATED`
TCGA-F2-7273 TCGA-IB-7651 TCGA-Q3-A5QY 
         360         1989          416 

$`FOXP2 WILD-TYPE`
TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         153          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-US-A776 
         110          844 

  FOXP2 MUTATED FOXP2 WILD-TYPE 
            360               1 
  FOXP2 MUTATED FOXP2 WILD-TYPE 
           1989            1991 
  FOXP2 MUTATED FOXP2 WILD-TYPE 
            416             233 
[1] "360.0 - 1989.0 (416.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "2.2"
D100V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  FOXP2 MUTATED          0         0         4         0        0
  FOXP2 WILD-TYPE        2         6        19         1        1
D100V3, multiclass
           clus
vv          FOXP2 MUTATED FOXP2 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             4              19
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  FOXP2 MUTATED          4
  FOXP2 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D100V5, binary
                 cls
clus               0  1
  FOXP2 MUTATED    0  4
  FOXP2 WILD-TYPE  7 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXP2 MUTATED      0    4
  FOXP2 WILD-TYPE    7   21
   clus
vv  FOXP2 MUTATED FOXP2 WILD-TYPE
  0             0               7
  1             4              21
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  FOXP2 MUTATED    3  0  1
  FOXP2 WILD-TYPE 16  1 12
D100V6, multiclass
    clus
vv   FOXP2 MUTATED FOXP2 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V7, binary
                 cls
clus               0  1
  FOXP2 MUTATED    1  3
  FOXP2 WILD-TYPE 13 16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXP2 MUTATED      1    3
  FOXP2 WILD-TYPE   13   16
        clus
vv       FOXP2 MUTATED FOXP2 WILD-TYPE
  FEMALE             1              13
  MALE               3              16
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  FOXP2 MUTATED                                     4
  FOXP2 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  FOXP2 MUTATED                                       0
  FOXP2 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  FOXP2 MUTATED                                                  0
  FOXP2 WILD-TYPE                                                2
D100V8, multiclass
                                                  clus
vv                                                 FOXP2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 FOXP2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V9, continuous
[1] "Remove cluster labels:" "FOXP2 MUTATED"         
clus
  FOXP2 MUTATED FOXP2 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"FOXP2 WILD-TYPE" "FOXP2 WILD-TYPE" "FOXP2 WILD-TYPE" "FOXP2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"FOXP2 WILD-TYPE" "FOXP2 WILD-TYPE" "FOXP2 WILD-TYPE" "FOXP2 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"FOXP2 WILD-TYPE" "FOXP2 WILD-TYPE" 
D100V10, binary
                 cls
clus               0  1
  FOXP2 MUTATED    3  1
  FOXP2 WILD-TYPE 21  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXP2 MUTATED      3    1
  FOXP2 WILD-TYPE   21    8
    clus
vv   FOXP2 MUTATED FOXP2 WILD-TYPE
  R0             3              21
  R1             1               8
[1] 2 2
[1] FALSE
D100V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXP2 MUTATED       0                         2     2
  FOXP2 WILD-TYPE     2                         1    26
D100V12, multiclass
                           clus
vv                          FOXP2 MUTATED FOXP2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2               1
  WHITE                                 2              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(101) Variable = NAPSA MUTATION ANALYSIS
D101V1, survival
                 sevent
clus2              0  1
  NAPSA MUTATED    1  1
  NAPSA WILD-TYPE 17  4
  NAPSA MUTATED NAPSA WILD-TYPE 
              2              21 
  NAPSA MUTATED NAPSA WILD-TYPE 
              1               4 
$`NAPSA MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 
         361         1989 

$`NAPSA WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  NAPSA MUTATED NAPSA WILD-TYPE 
            361               1 
  NAPSA MUTATED NAPSA WILD-TYPE 
           1989            1991 
  NAPSA MUTATED NAPSA WILD-TYPE 
           1175             300 
[1] "361.0 - 1989.0 (1175.0)" "1.0 - 1991.0 (300.0)"   
[1] "Remove cluster labels:" "NAPSA MUTATED"         
D101V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  NAPSA MUTATED          0         1         2         0        0
  NAPSA WILD-TYPE        2         5        21         1        1
D101V3, multiclass
           clus
vv          NAPSA MUTATED NAPSA WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  NAPSA MUTATED          3
  NAPSA WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D101V5, binary
                 cls
clus               0  1
  NAPSA MUTATED    1  2
  NAPSA WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAPSA MUTATED      1    2
  NAPSA WILD-TYPE    6   23
   clus
vv  NAPSA MUTATED NAPSA WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  NAPSA MUTATED    2  0  1
  NAPSA WILD-TYPE 17  1 12
D101V6, multiclass
    clus
vv   NAPSA MUTATED NAPSA WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V7, binary
                 cls
clus               0  1
  NAPSA MUTATED    1  2
  NAPSA WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAPSA MUTATED      1    2
  NAPSA WILD-TYPE   13   17
        clus
vv       NAPSA MUTATED NAPSA WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  NAPSA MUTATED                                     3
  NAPSA WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  NAPSA MUTATED                                       0
  NAPSA WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  NAPSA MUTATED                                                  0
  NAPSA WILD-TYPE                                                2
D101V8, multiclass
                                                  clus
vv                                                 NAPSA MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 NAPSA WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V9, continuous
[1] "Remove cluster labels:" "NAPSA MUTATED"         
clus
  NAPSA MUTATED NAPSA WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"NAPSA WILD-TYPE" "NAPSA WILD-TYPE" "NAPSA WILD-TYPE" "NAPSA WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"NAPSA WILD-TYPE" "NAPSA WILD-TYPE" "NAPSA WILD-TYPE" "NAPSA WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"NAPSA WILD-TYPE" "NAPSA WILD-TYPE" 
D101V10, binary
                 cls
clus               0  1
  NAPSA MUTATED    3  0
  NAPSA WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAPSA MUTATED      3    0
  NAPSA WILD-TYPE   21    9
    clus
vv   NAPSA MUTATED NAPSA WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D101V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NAPSA MUTATED       0                         0     3
  NAPSA WILD-TYPE     2                         3    25
D101V12, multiclass
                           clus
vv                          NAPSA MUTATED NAPSA WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(102) Variable = EIF3C MUTATION ANALYSIS
D102V1, survival
                 sevent
clus2              0  1
  EIF3C MUTATED    1  1
  EIF3C WILD-TYPE 17  4
  EIF3C MUTATED EIF3C WILD-TYPE 
              2              21 
  EIF3C MUTATED EIF3C WILD-TYPE 
              1               4 
$`EIF3C MUTATED`
TCGA-IB-7651 TCGA-IB-A5ST 
        1989            8 

$`EIF3C WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UG TCGA-LB-A7SX 
          17          329          300         1991         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  EIF3C MUTATED EIF3C WILD-TYPE 
              8               1 
  EIF3C MUTATED EIF3C WILD-TYPE 
           1989            1991 
  EIF3C MUTATED EIF3C WILD-TYPE 
          998.5           329.0 
[1] "8.0 - 1989.0 (998.5)" "1.0 - 1991.0 (329.0)"
[1] "Remove cluster labels:" "EIF3C MUTATED"         
D102V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  EIF3C MUTATED          0         0         3         0        0
  EIF3C WILD-TYPE        2         6        20         1        1
D102V3, multiclass
           clus
vv          EIF3C MUTATED EIF3C WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  EIF3C MUTATED          3
  EIF3C WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D102V5, binary
                 cls
clus               0  1
  EIF3C MUTATED    0  3
  EIF3C WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF3C MUTATED      0    3
  EIF3C WILD-TYPE    7   22
   clus
vv  EIF3C MUTATED EIF3C WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  EIF3C MUTATED    2  0  1
  EIF3C WILD-TYPE 17  1 12
D102V6, multiclass
    clus
vv   EIF3C MUTATED EIF3C WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V7, binary
                 cls
clus               0  1
  EIF3C MUTATED    2  1
  EIF3C WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF3C MUTATED      2    1
  EIF3C WILD-TYPE   12   18
        clus
vv       EIF3C MUTATED EIF3C WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  EIF3C MUTATED                                     2
  EIF3C WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  EIF3C MUTATED                                       1
  EIF3C WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  EIF3C MUTATED                                                  0
  EIF3C WILD-TYPE                                                2
D102V8, multiclass
                                                  clus
vv                                                 EIF3C MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 EIF3C WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V9, continuous
[1] "Remove cluster labels:" "EIF3C MUTATED"         
clus
  EIF3C MUTATED EIF3C WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"EIF3C WILD-TYPE" "EIF3C WILD-TYPE" "EIF3C WILD-TYPE" "EIF3C WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"EIF3C WILD-TYPE" "EIF3C WILD-TYPE" "EIF3C WILD-TYPE" "EIF3C WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"EIF3C WILD-TYPE" "EIF3C WILD-TYPE" 
D102V10, binary
                 cls
clus               0  1
  EIF3C MUTATED    2  1
  EIF3C WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF3C MUTATED      2    1
  EIF3C WILD-TYPE   22    8
    clus
vv   EIF3C MUTATED EIF3C WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D102V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EIF3C MUTATED       0                         0     3
  EIF3C WILD-TYPE     2                         3    25
D102V12, multiclass
                           clus
vv                          EIF3C MUTATED EIF3C WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(103) Variable = GTF2F1 MUTATION ANALYSIS
D103V1, survival
                  sevent
clus2               0  1
  GTF2F1 MUTATED    0  2
  GTF2F1 WILD-TYPE 18  3
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               2               21 
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               2                3 
$`GTF2F1 MUTATED`
TCGA-F2-A44G TCGA-IB-7651 
         153         1989 

$`GTF2F1 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
             153                1 
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
            1989             1991 
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
            1071              329 
[1] "153.0 - 1989.0 (1071.0)" "1.0 - 1991.0 (329.0)"   
[1] "Remove cluster labels:" "GTF2F1 MUTATED"        
D103V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GTF2F1 MUTATED          1         0         2         0        0
  GTF2F1 WILD-TYPE        1         6        21         1        1
D103V3, multiclass
           clus
vv          GTF2F1 MUTATED GTF2F1 WILD-TYPE
  STAGE IB               1                1
  STAGE IIA              0                6
  STAGE IIB              2               21
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  GTF2F1 MUTATED          3
  GTF2F1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D103V5, binary
                  cls
clus                0  1
  GTF2F1 MUTATED    1  2
  GTF2F1 WILD-TYPE  6 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2F1 MUTATED      1    2
  GTF2F1 WILD-TYPE    6   23
   clus
vv  GTF2F1 MUTATED GTF2F1 WILD-TYPE
  0              1                6
  1              2               23
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  GTF2F1 MUTATED    3  0  0
  GTF2F1 WILD-TYPE 16  1 13
D103V6, multiclass
    clus
vv   GTF2F1 MUTATED GTF2F1 WILD-TYPE
  M0              3               16
  M1              0                1
  MX              0               13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V7, binary
                  cls
clus                0  1
  GTF2F1 MUTATED    3  0
  GTF2F1 WILD-TYPE 11 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2F1 MUTATED      3    0
  GTF2F1 WILD-TYPE   11   19
        clus
vv       GTF2F1 MUTATED GTF2F1 WILD-TYPE
  FEMALE              3               11
  MALE                0               19
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GTF2F1 MUTATED                                     3
  GTF2F1 WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GTF2F1 MUTATED                                       0
  GTF2F1 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GTF2F1 MUTATED                                                  0
  GTF2F1 WILD-TYPE                                                2
D103V8, multiclass
                                                  clus
vv                                                 GTF2F1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 GTF2F1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V9, continuous
[1] "Remove cluster labels:" "GTF2F1 MUTATED"        
clus
  GTF2F1 MUTATED GTF2F1 WILD-TYPE 
               1               10 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-H8-A6C1 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A5SS       TCGA-IB-A6UG 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
      TCGA-LB-A7SX       TCGA-OE-A75W 
"GTF2F1 WILD-TYPE" "GTF2F1 WILD-TYPE" 
D103V10, binary
                  cls
clus                0  1
  GTF2F1 MUTATED    2  1
  GTF2F1 WILD-TYPE 22  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF2F1 MUTATED      2    1
  GTF2F1 WILD-TYPE   22    8
    clus
vv   GTF2F1 MUTATED GTF2F1 WILD-TYPE
  R0              2               22
  R1              1                8
[1] 2 2
[1] FALSE
D103V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GTF2F1 MUTATED       0                         0     3
  GTF2F1 WILD-TYPE     2                         3    25
D103V12, multiclass
                           clus
vv                          GTF2F1 MUTATED GTF2F1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(104) Variable = CCKAR MUTATION ANALYSIS
D104V1, survival
                 sevent
clus2              0  1
  CCKAR MUTATED    0  1
  CCKAR WILD-TYPE 18  4
  CCKAR MUTATED CCKAR WILD-TYPE 
              1              22 
  CCKAR MUTATED CCKAR WILD-TYPE 
              1               4 
$`CCKAR MUTATED`
TCGA-IB-7651 
        1989 

$`CCKAR WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         127          110          416          844 

  CCKAR MUTATED CCKAR WILD-TYPE 
           1989               1 
  CCKAR MUTATED CCKAR WILD-TYPE 
           1989            1991 
  CCKAR MUTATED CCKAR WILD-TYPE 
         1989.0           314.5 
[1] "1989.0 - 1989.0 (1989.0)" "1.0 - 1991.0 (314.5)"    
[1] "Remove cluster labels:" "CCKAR MUTATED"         
D104V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CCKAR MUTATED          0         0         2         0        1
  CCKAR WILD-TYPE        2         6        21         1        0
D104V3, multiclass
           clus
vv          CCKAR MUTATED CCKAR WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              1               0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  CCKAR MUTATED          3
  CCKAR WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D104V5, binary
                 cls
clus               0  1
  CCKAR MUTATED    0  3
  CCKAR WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCKAR MUTATED      0    3
  CCKAR WILD-TYPE    7   22
   clus
vv  CCKAR MUTATED CCKAR WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  CCKAR MUTATED    1  1  1
  CCKAR WILD-TYPE 18  0 12
D104V6, multiclass
    clus
vv   CCKAR MUTATED CCKAR WILD-TYPE
  M0             1              18
  M1             1               0
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V7, binary
                 cls
clus               0  1
  CCKAR MUTATED    2  1
  CCKAR WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCKAR MUTATED      2    1
  CCKAR WILD-TYPE   12   18
        clus
vv       CCKAR MUTATED CCKAR WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCKAR MUTATED                                     3
  CCKAR WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCKAR MUTATED                                       0
  CCKAR WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCKAR MUTATED                                                  0
  CCKAR WILD-TYPE                                                2
D104V8, multiclass
                                                  clus
vv                                                 CCKAR MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CCKAR WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V9, continuous
[1] "Remove cluster labels:" "CCKAR MUTATED"         
clus
  CCKAR MUTATED CCKAR WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"CCKAR WILD-TYPE" "CCKAR WILD-TYPE" 
D104V10, binary
                 cls
clus               0  1
  CCKAR MUTATED    3  0
  CCKAR WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCKAR MUTATED      3    0
  CCKAR WILD-TYPE   21    9
    clus
vv   CCKAR MUTATED CCKAR WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D104V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCKAR MUTATED       0                         0     3
  CCKAR WILD-TYPE     2                         3    25
D104V12, multiclass
                           clus
vv                          CCKAR MUTATED CCKAR WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(105) Variable = MMP14 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2              0  1
  MMP14 MUTATED    1  1
  MMP14 WILD-TYPE 17  4
  MMP14 MUTATED MMP14 WILD-TYPE 
              2              21 
  MMP14 MUTATED MMP14 WILD-TYPE 
              1               4 
$`MMP14 MUTATED`
TCGA-FB-A78T TCGA-IB-7651 
           1         1989 

$`MMP14 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  MMP14 MUTATED MMP14 WILD-TYPE 
              1               8 
  MMP14 MUTATED MMP14 WILD-TYPE 
           1989            1991 
  MMP14 MUTATED MMP14 WILD-TYPE 
            995             329 
[1] "1.0 - 1989.0 (995.0)" "8.0 - 1991.0 (329.0)"
[1] "Remove cluster labels:" "MMP14 MUTATED"         
D105V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  MMP14 MUTATED          0         0         3         0        0
  MMP14 WILD-TYPE        2         6        20         1        1
D105V3, multiclass
           clus
vv          MMP14 MUTATED MMP14 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  MMP14 MUTATED          3
  MMP14 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D105V5, binary
                 cls
clus               0  1
  MMP14 MUTATED    0  3
  MMP14 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP14 MUTATED      0    3
  MMP14 WILD-TYPE    7   22
   clus
vv  MMP14 MUTATED MMP14 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  MMP14 MUTATED    2  0  1
  MMP14 WILD-TYPE 17  1 12
D105V6, multiclass
    clus
vv   MMP14 MUTATED MMP14 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V7, binary
                 cls
clus               0  1
  MMP14 MUTATED    3  0
  MMP14 WILD-TYPE 11 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP14 MUTATED      3    0
  MMP14 WILD-TYPE   11   19
        clus
vv       MMP14 MUTATED MMP14 WILD-TYPE
  FEMALE             3              11
  MALE               0              19
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  MMP14 MUTATED                                     3
  MMP14 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  MMP14 MUTATED                                       0
  MMP14 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  MMP14 MUTATED                                                  0
  MMP14 WILD-TYPE                                                2
D105V8, multiclass
                                                  clus
vv                                                 MMP14 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 MMP14 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V9, continuous
[1] "Remove cluster labels:" "MMP14 MUTATED"         
clus
  MMP14 MUTATED MMP14 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A7DR      TCGA-H8-A6C1      TCGA-IB-7885 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" "MMP14 WILD-TYPE" 
     TCGA-OE-A75W 
"MMP14 WILD-TYPE" 
D105V10, binary
                 cls
clus               0  1
  MMP14 MUTATED    3  0
  MMP14 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP14 MUTATED      3    0
  MMP14 WILD-TYPE   21    9
    clus
vv   MMP14 MUTATED MMP14 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D105V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MMP14 MUTATED       0                         0     3
  MMP14 WILD-TYPE     2                         3    25
D105V12, multiclass
                           clus
vv                          MMP14 MUTATED MMP14 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(106) Variable = ATM MUTATION ANALYSIS
D106V1, survival
               sevent
clus2            0  1
  ATM MUTATED    1  1
  ATM WILD-TYPE 17  4
  ATM MUTATED ATM WILD-TYPE 
            2            21 
  ATM MUTATED ATM WILD-TYPE 
            1             4 
$`ATM MUTATED`
TCGA-IB-7651 TCGA-US-A776 
        1989          844 

$`ATM WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY 
         127          110          416 

  ATM MUTATED ATM WILD-TYPE 
          844             1 
  ATM MUTATED ATM WILD-TYPE 
         1989          1991 
  ATM MUTATED ATM WILD-TYPE 
       1416.5         300.0 
[1] "844.0 - 1989.0 (1416.5)" "1.0 - 1991.0 (300.0)"   
[1] "Remove cluster labels:" "ATM MUTATED"           
D106V2, continuous
               vv
clus            STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ATM MUTATED          0         1         1         0        1
  ATM WILD-TYPE        2         5        22         1        0
D106V3, multiclass
           clus
vv          ATM MUTATED ATM WILD-TYPE
  STAGE IB            0             2
  STAGE IIA           1             5
  STAGE IIB           1            22
  STAGE III           0             1
  STAGE IV            1             0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T2+T3+T4
  ATM MUTATED          3
  ATM WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D106V5, binary
               cls
clus             0  1
  ATM MUTATED    1  2
  ATM WILD-TYPE  6 23
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1    2
  ATM WILD-TYPE    6   23
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0           1             6
  1           2            23
[1] 2 2
[1] FALSE
               vv
clus            M0 M1 MX
  ATM MUTATED    1  1  1
  ATM WILD-TYPE 18  0 12
D106V6, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  M0           1            18
  M1           1             0
  MX           1            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V7, binary
               cls
clus             0  1
  ATM MUTATED    1  2
  ATM WILD-TYPE 13 17
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1    2
  ATM WILD-TYPE   13   17
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE           1            13
  MALE             2            17
[1] 2 2
[1] FALSE
               vv
clus            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ATM MUTATED                                     2
  ATM WILD-TYPE                                  26
               vv
clus            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ATM MUTATED                                       0
  ATM WILD-TYPE                                     3
               vv
clus            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ATM MUTATED                                                  1
  ATM WILD-TYPE                                                1
D106V8, multiclass
                                                  clus
vv                                                 ATM MUTATED ATM WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                        2            26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                      0             3
  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"
D106V9, continuous
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            1            10 
   TCGA-FB-A5VM    TCGA-FB-A78T    TCGA-FB-A7DR    TCGA-H8-A6C1    TCGA-IB-7885 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-IB-8126    TCGA-IB-A5SS    TCGA-IB-A6UG    TCGA-LB-A7SX    TCGA-OE-A75W 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
D106V10, binary
               cls
clus             0  1
  ATM MUTATED    3  0
  ATM WILD-TYPE 21  9
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      3    0
  ATM WILD-TYPE   21    9
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0           3            21
  R1           0             9
[1] 2 2
[1] FALSE
D106V11, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       0                         0     3
  ATM WILD-TYPE     2                         3    25
D106V12, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0             3
  WHITE                               3            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(107) Variable = IFFO1 MUTATION ANALYSIS
D107V1, survival
                 sevent
clus2              0  1
  IFFO1 MUTATED    2  1
  IFFO1 WILD-TYPE 16  4
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              3              20 
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              1               4 
$`IFFO1 MUTATED`
TCGA-H8-A6C1 TCGA-IB-7651 TCGA-US-A776 
         396         1989          844 

$`IFFO1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY 
         110          416 

  IFFO1 MUTATED IFFO1 WILD-TYPE 
            396               1 
  IFFO1 MUTATED IFFO1 WILD-TYPE 
           1989            1991 
  IFFO1 MUTATED IFFO1 WILD-TYPE 
            844             233 
[1] "396.0 - 1989.0 (844.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D107V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  IFFO1 MUTATED          0         2         1         0        0
  IFFO1 WILD-TYPE        2         4        22         1        1
D107V3, multiclass
           clus
vv          IFFO1 MUTATED IFFO1 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             2               4
  STAGE IIB             1              22
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  IFFO1 MUTATED          3
  IFFO1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D107V5, binary
                 cls
clus               0  1
  IFFO1 MUTATED    2  1
  IFFO1 WILD-TYPE  5 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFFO1 MUTATED      2    1
  IFFO1 WILD-TYPE    5   24
   clus
vv  IFFO1 MUTATED IFFO1 WILD-TYPE
  0             2               5
  1             1              24
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  IFFO1 MUTATED    1  0  2
  IFFO1 WILD-TYPE 18  1 11
D107V6, multiclass
    clus
vv   IFFO1 MUTATED IFFO1 WILD-TYPE
  M0             1              18
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V7, binary
                 cls
clus               0  1
  IFFO1 MUTATED    1  2
  IFFO1 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFFO1 MUTATED      1    2
  IFFO1 WILD-TYPE   13   17
        clus
vv       IFFO1 MUTATED IFFO1 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IFFO1 MUTATED                                     1
  IFFO1 WILD-TYPE                                  27
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IFFO1 MUTATED                                       1
  IFFO1 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IFFO1 MUTATED                                                  1
  IFFO1 WILD-TYPE                                                1
D107V8, multiclass
                                                  clus
vv                                                 IFFO1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          1
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             1
                                                  clus
vv                                                 IFFO1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           27
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  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"
D107V9, continuous
[1] "Remove cluster labels:" "IFFO1 MUTATED"         
clus
  IFFO1 MUTATED IFFO1 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-IB-7885 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" "IFFO1 WILD-TYPE" 
     TCGA-OE-A75W 
"IFFO1 WILD-TYPE" 
D107V10, binary
                 cls
clus               0  1
  IFFO1 MUTATED    3  0
  IFFO1 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFFO1 MUTATED      3    0
  IFFO1 WILD-TYPE   21    9
    clus
vv   IFFO1 MUTATED IFFO1 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D107V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFFO1 MUTATED       0                         0     3
  IFFO1 WILD-TYPE     2                         3    25
D107V12, multiclass
                           clus
vv                          IFFO1 MUTATED IFFO1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(108) Variable = TWISTNB MUTATION ANALYSIS
D108V1, survival
                   sevent
clus2                0  1
  TWISTNB MUTATED    1  2
  TWISTNB WILD-TYPE 17  3
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                3                20 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                2                 3 
$`TWISTNB MUTATED`
TCGA-F2-A44G TCGA-FB-A7DR TCGA-IB-7651 
         153          166         1989 

$`TWISTNB WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7925 
         360          449            1          396           28          361 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
          11           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  TWISTNB MUTATED TWISTNB WILD-TYPE 
              153                 1 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
             1989              1991 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
            166.0             344.5 
[1] "153.0 - 1989.0 (166.0)" "1.0 - 1991.0 (344.5)"  
[1] "hr=" "3"  
D108V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TWISTNB MUTATED          0         1         2         0        0
  TWISTNB WILD-TYPE        2         5        21         1        1
D108V3, multiclass
           clus
vv          TWISTNB MUTATED TWISTNB WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               1                 5
  STAGE IIB               2                21
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  TWISTNB MUTATED          3
  TWISTNB WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D108V5, binary
                   cls
clus                 0  1
  TWISTNB MUTATED    0  2
  TWISTNB WILD-TYPE  7 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      0    2
  TWISTNB WILD-TYPE    7   23
   clus
vv  TWISTNB MUTATED TWISTNB WILD-TYPE
  0               0                 7
  1               2                23
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  TWISTNB MUTATED    3  0  0
  TWISTNB WILD-TYPE 16  1 13
D108V6, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  M0               3                16
  M1               0                 1
  MX               0                13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V7, binary
                   cls
clus                 0  1
  TWISTNB MUTATED    2  1
  TWISTNB WILD-TYPE 12 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      2    1
  TWISTNB WILD-TYPE   12   18
        clus
vv       TWISTNB MUTATED TWISTNB WILD-TYPE
  FEMALE               2                12
  MALE                 1                18
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TWISTNB MUTATED                                     2
  TWISTNB WILD-TYPE                                  26
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TWISTNB MUTATED                                       0
  TWISTNB WILD-TYPE                                     3
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TWISTNB MUTATED                                                  1
  TWISTNB WILD-TYPE                                                1
D108V8, multiclass
                                                  clus
vv                                                 TWISTNB MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 TWISTNB WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            3
  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"
D108V9, continuous
[1] "Remove cluster labels:" "TWISTNB MUTATED"       
clus
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                2                 9 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-H8-A6C1        TCGA-IB-7885 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-LB-A7SX 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-OE-A75W 
"TWISTNB WILD-TYPE" 
D108V10, binary
                   cls
clus                 0  1
  TWISTNB MUTATED    2  1
  TWISTNB WILD-TYPE 22  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      2    1
  TWISTNB WILD-TYPE   22    8
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  R0               2                22
  R1               1                 8
[1] 2 2
[1] FALSE
D108V11, continuous
[1] "Remove cluster labels:" "TWISTNB MUTATED"       
clus
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                2                30 
       TCGA-F2-7273        TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FZ-5920 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-FZ-5922        TCGA-FZ-5923        TCGA-H8-A6C1        TCGA-HZ-7918 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-HZ-7925        TCGA-HZ-8637        TCGA-HZ-A49I        TCGA-HZ-A77O 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-HZ-A77P        TCGA-IB-7652        TCGA-IB-7885        TCGA-IB-8126 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-IB-A5SO        TCGA-IB-A5SP        TCGA-IB-A5SQ        TCGA-IB-A5SS 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-IB-A5ST        TCGA-IB-A6UG        TCGA-LB-A7SX        TCGA-OE-A75W 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-Q3-A5QY        TCGA-US-A776        TCGA-US-A779        TCGA-US-A77E 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
       TCGA-US-A77G        TCGA-US-A77J 
"TWISTNB WILD-TYPE" "TWISTNB WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TWISTNB MUTATED       1                         0     2
  TWISTNB WILD-TYPE     1                         3    26
D108V12, multiclass
                           clus
vv                          TWISTNB MUTATED TWISTNB WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   2                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(109) Variable = SPAG9 MUTATION ANALYSIS
D109V1, survival
                 sevent
clus2              0  1
  SPAG9 MUTATED    1  1
  SPAG9 WILD-TYPE 17  4
  SPAG9 MUTATED SPAG9 WILD-TYPE 
              2              21 
  SPAG9 MUTATED SPAG9 WILD-TYPE 
              1               4 
$`SPAG9 MUTATED`
TCGA-IB-7651 TCGA-IB-A5ST 
        1989            8 

$`SPAG9 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UG TCGA-LB-A7SX 
          17          329          300         1991         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  SPAG9 MUTATED SPAG9 WILD-TYPE 
              8               1 
  SPAG9 MUTATED SPAG9 WILD-TYPE 
           1989            1991 
  SPAG9 MUTATED SPAG9 WILD-TYPE 
          998.5           329.0 
[1] "8.0 - 1989.0 (998.5)" "1.0 - 1991.0 (329.0)"
[1] "Remove cluster labels:" "SPAG9 MUTATED"         
D109V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SPAG9 MUTATED          0         0         3         0        0
  SPAG9 WILD-TYPE        2         6        20         1        1
D109V3, multiclass
           clus
vv          SPAG9 MUTATED SPAG9 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  SPAG9 MUTATED          3
  SPAG9 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D109V5, binary
                 cls
clus               0  1
  SPAG9 MUTATED    0  3
  SPAG9 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG9 MUTATED      0    3
  SPAG9 WILD-TYPE    7   22
   clus
vv  SPAG9 MUTATED SPAG9 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  SPAG9 MUTATED    2  0  1
  SPAG9 WILD-TYPE 17  1 12
D109V6, multiclass
    clus
vv   SPAG9 MUTATED SPAG9 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V7, binary
                 cls
clus               0  1
  SPAG9 MUTATED    2  1
  SPAG9 WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG9 MUTATED      2    1
  SPAG9 WILD-TYPE   12   18
        clus
vv       SPAG9 MUTATED SPAG9 WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SPAG9 MUTATED                                     3
  SPAG9 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SPAG9 MUTATED                                       0
  SPAG9 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SPAG9 MUTATED                                                  0
  SPAG9 WILD-TYPE                                                2
D109V8, multiclass
                                                  clus
vv                                                 SPAG9 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SPAG9 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V9, continuous
[1] "Remove cluster labels:" "SPAG9 MUTATED"         
clus
  SPAG9 MUTATED SPAG9 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"SPAG9 WILD-TYPE" "SPAG9 WILD-TYPE" "SPAG9 WILD-TYPE" "SPAG9 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"SPAG9 WILD-TYPE" "SPAG9 WILD-TYPE" "SPAG9 WILD-TYPE" "SPAG9 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"SPAG9 WILD-TYPE" "SPAG9 WILD-TYPE" 
D109V10, binary
                 cls
clus               0  1
  SPAG9 MUTATED    2  1
  SPAG9 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG9 MUTATED      2    1
  SPAG9 WILD-TYPE   22    8
    clus
vv   SPAG9 MUTATED SPAG9 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D109V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPAG9 MUTATED       0                         0     3
  SPAG9 WILD-TYPE     2                         3    25
D109V12, multiclass
                           clus
vv                          SPAG9 MUTATED SPAG9 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(110) Variable = SMCR7 MUTATION ANALYSIS
D110V1, survival
                 sevent
clus2              0  1
  SMCR7 MUTATED    1  1
  SMCR7 WILD-TYPE 17  4
  SMCR7 MUTATED SMCR7 WILD-TYPE 
              2              21 
  SMCR7 MUTATED SMCR7 WILD-TYPE 
              1               4 
$`SMCR7 MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 
         361         1989 

$`SMCR7 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  SMCR7 MUTATED SMCR7 WILD-TYPE 
            361               1 
  SMCR7 MUTATED SMCR7 WILD-TYPE 
           1989            1991 
  SMCR7 MUTATED SMCR7 WILD-TYPE 
           1175             300 
[1] "361.0 - 1989.0 (1175.0)" "1.0 - 1991.0 (300.0)"   
[1] "Remove cluster labels:" "SMCR7 MUTATED"         
D110V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SMCR7 MUTATED          0         0         3         0        0
  SMCR7 WILD-TYPE        2         6        20         1        1
D110V3, multiclass
           clus
vv          SMCR7 MUTATED SMCR7 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  SMCR7 MUTATED          3
  SMCR7 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D110V5, binary
                 cls
clus               0  1
  SMCR7 MUTATED    0  3
  SMCR7 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMCR7 MUTATED      0    3
  SMCR7 WILD-TYPE    7   22
   clus
vv  SMCR7 MUTATED SMCR7 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  SMCR7 MUTATED    1  0  2
  SMCR7 WILD-TYPE 18  1 11
D110V6, multiclass
    clus
vv   SMCR7 MUTATED SMCR7 WILD-TYPE
  M0             1              18
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V7, binary
                 cls
clus               0  1
  SMCR7 MUTATED    1  2
  SMCR7 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMCR7 MUTATED      1    2
  SMCR7 WILD-TYPE   13   17
        clus
vv       SMCR7 MUTATED SMCR7 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMCR7 MUTATED                                     3
  SMCR7 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMCR7 MUTATED                                       0
  SMCR7 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMCR7 MUTATED                                                  0
  SMCR7 WILD-TYPE                                                2
D110V8, multiclass
                                                  clus
vv                                                 SMCR7 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SMCR7 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V9, continuous
[1] "Remove cluster labels:" "SMCR7 MUTATED"         
clus
  SMCR7 MUTATED SMCR7 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"SMCR7 WILD-TYPE" "SMCR7 WILD-TYPE" "SMCR7 WILD-TYPE" "SMCR7 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"SMCR7 WILD-TYPE" "SMCR7 WILD-TYPE" "SMCR7 WILD-TYPE" "SMCR7 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"SMCR7 WILD-TYPE" "SMCR7 WILD-TYPE" 
D110V10, binary
                 cls
clus               0  1
  SMCR7 MUTATED    3  0
  SMCR7 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMCR7 MUTATED      3    0
  SMCR7 WILD-TYPE   21    9
    clus
vv   SMCR7 MUTATED SMCR7 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D110V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMCR7 MUTATED       0                         0     3
  SMCR7 WILD-TYPE     2                         3    25
D110V12, multiclass
                           clus
vv                          SMCR7 MUTATED SMCR7 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(111) Variable = PSAT1 MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2              0  1
  PSAT1 MUTATED    0  1
  PSAT1 WILD-TYPE 18  4
  PSAT1 MUTATED PSAT1 WILD-TYPE 
              1              22 
  PSAT1 MUTATED PSAT1 WILD-TYPE 
              1               4 
$`PSAT1 MUTATED`
TCGA-IB-A5SS 
        1991 

$`PSAT1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 
          28          361           11           13         1989          476 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UG 
         851           17          329          300            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         127          110          416          844 

  PSAT1 MUTATED PSAT1 WILD-TYPE 
           1991               1 
  PSAT1 MUTATED PSAT1 WILD-TYPE 
           1991            1989 
  PSAT1 MUTATED PSAT1 WILD-TYPE 
         1991.0           314.5 
[1] "1991.0 - 1991.0 (1991.0)" "1.0 - 1989.0 (314.5)"    
[1] "Remove cluster labels:" "PSAT1 MUTATED"         
D111V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PSAT1 MUTATED          0         1         2         0        0
  PSAT1 WILD-TYPE        2         5        21         1        1
D111V3, multiclass
           clus
vv          PSAT1 MUTATED PSAT1 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  PSAT1 MUTATED          3
  PSAT1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D111V5, binary
                 cls
clus               0  1
  PSAT1 MUTATED    1  2
  PSAT1 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSAT1 MUTATED      1    2
  PSAT1 WILD-TYPE    6   23
   clus
vv  PSAT1 MUTATED PSAT1 WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  PSAT1 MUTATED    2  0  1
  PSAT1 WILD-TYPE 17  1 12
D111V6, multiclass
    clus
vv   PSAT1 MUTATED PSAT1 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V7, binary
                 cls
clus               0  1
  PSAT1 MUTATED    1  2
  PSAT1 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSAT1 MUTATED      1    2
  PSAT1 WILD-TYPE   13   17
        clus
vv       PSAT1 MUTATED PSAT1 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PSAT1 MUTATED                                     3
  PSAT1 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PSAT1 MUTATED                                       0
  PSAT1 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PSAT1 MUTATED                                                  0
  PSAT1 WILD-TYPE                                                2
D111V8, multiclass
                                                  clus
vv                                                 PSAT1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PSAT1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V9, continuous
[1] "Remove cluster labels:" "PSAT1 MUTATED"         
clus
  PSAT1 MUTATED PSAT1 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"PSAT1 WILD-TYPE" "PSAT1 WILD-TYPE" "PSAT1 WILD-TYPE" "PSAT1 WILD-TYPE" 
     TCGA-IB-7651      TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A6UG 
"PSAT1 WILD-TYPE" "PSAT1 WILD-TYPE" "PSAT1 WILD-TYPE" "PSAT1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"PSAT1 WILD-TYPE" "PSAT1 WILD-TYPE" 
D111V10, binary
                 cls
clus               0  1
  PSAT1 MUTATED    3  0
  PSAT1 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSAT1 MUTATED      3    0
  PSAT1 WILD-TYPE   21    9
    clus
vv   PSAT1 MUTATED PSAT1 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D111V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSAT1 MUTATED       0                         0     3
  PSAT1 WILD-TYPE     2                         3    25
D111V12, multiclass
                           clus
vv                          PSAT1 MUTATED PSAT1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(112) Variable = PDILT MUTATION ANALYSIS
D112V1, survival
                 sevent
clus2              0  1
  PDILT MUTATED    2  1
  PDILT WILD-TYPE 16  4
  PDILT MUTATED PDILT WILD-TYPE 
              3              20 
  PDILT MUTATED PDILT WILD-TYPE 
              1               4 
$`PDILT MUTATED`
TCGA-HZ-7925 TCGA-IB-7651 TCGA-LB-A7SX 
         361         1989          127 

$`PDILT WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W 
         329          300         1991            8         1968          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  PDILT MUTATED PDILT WILD-TYPE 
            127               1 
  PDILT MUTATED PDILT WILD-TYPE 
           1989            1991 
  PDILT MUTATED PDILT WILD-TYPE 
          361.0           314.5 
[1] "127.0 - 1989.0 (361.0)" "1.0 - 1991.0 (314.5)"  
[1] "hr=" "1.2"
D112V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PDILT MUTATED          0         0         3         0        0
  PDILT WILD-TYPE        2         6        20         1        1
D112V3, multiclass
           clus
vv          PDILT MUTATED PDILT WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  PDILT MUTATED          3
  PDILT WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D112V5, binary
                 cls
clus               0  1
  PDILT MUTATED    0  3
  PDILT WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDILT MUTATED      0    3
  PDILT WILD-TYPE    7   22
   clus
vv  PDILT MUTATED PDILT WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  PDILT MUTATED    1  0  2
  PDILT WILD-TYPE 18  1 11
D112V6, multiclass
    clus
vv   PDILT MUTATED PDILT WILD-TYPE
  M0             1              18
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V7, binary
                 cls
clus               0  1
  PDILT MUTATED    2  1
  PDILT WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDILT MUTATED      2    1
  PDILT WILD-TYPE   12   18
        clus
vv       PDILT MUTATED PDILT WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDILT MUTATED                                     3
  PDILT WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDILT MUTATED                                       0
  PDILT WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDILT MUTATED                                                  0
  PDILT WILD-TYPE                                                2
D112V8, multiclass
                                                  clus
vv                                                 PDILT MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PDILT WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V9, continuous
[1] "Remove cluster labels:" "PDILT MUTATED"         
clus
  PDILT MUTATED PDILT WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" "PDILT WILD-TYPE" 
     TCGA-OE-A75W 
"PDILT WILD-TYPE" 
D112V10, binary
                 cls
clus               0  1
  PDILT MUTATED    2  1
  PDILT WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDILT MUTATED      2    1
  PDILT WILD-TYPE   22    8
    clus
vv   PDILT MUTATED PDILT WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D112V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDILT MUTATED       0                         1     2
  PDILT WILD-TYPE     2                         2    26
D112V12, multiclass
                           clus
vv                          PDILT MUTATED PDILT WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               2
  WHITE                                 2              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(113) Variable = CCDC8 MUTATION ANALYSIS
D113V1, survival
                 sevent
clus2              0  1
  CCDC8 MUTATED    2  1
  CCDC8 WILD-TYPE 16  4
  CCDC8 MUTATED CCDC8 WILD-TYPE 
              3              20 
  CCDC8 MUTATED CCDC8 WILD-TYPE 
              1               4 
$`CCDC8 MUTATED`
TCGA-IB-7651 TCGA-IB-A5ST TCGA-Q3-A5QY 
        1989            8          416 

$`CCDC8 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UG TCGA-LB-A7SX 
          17          329          300         1991         1968          127 
TCGA-OE-A75W TCGA-US-A776 
         110          844 

  CCDC8 MUTATED CCDC8 WILD-TYPE 
              8               1 
  CCDC8 MUTATED CCDC8 WILD-TYPE 
           1989            1991 
  CCDC8 MUTATED CCDC8 WILD-TYPE 
          416.0           314.5 
[1] "8.0 - 1989.0 (416.0)" "1.0 - 1991.0 (314.5)"
[1] "hr=" "1.2"
D113V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CCDC8 MUTATED          0         0         3         0        0
  CCDC8 WILD-TYPE        2         6        20         1        1
D113V3, multiclass
           clus
vv          CCDC8 MUTATED CCDC8 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  CCDC8 MUTATED          3
  CCDC8 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D113V5, binary
                 cls
clus               0  1
  CCDC8 MUTATED    0  3
  CCDC8 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC8 MUTATED      0    3
  CCDC8 WILD-TYPE    7   22
   clus
vv  CCDC8 MUTATED CCDC8 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  CCDC8 MUTATED    2  0  1
  CCDC8 WILD-TYPE 17  1 12
D113V6, multiclass
    clus
vv   CCDC8 MUTATED CCDC8 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V7, binary
                 cls
clus               0  1
  CCDC8 MUTATED    2  1
  CCDC8 WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC8 MUTATED      2    1
  CCDC8 WILD-TYPE   12   18
        clus
vv       CCDC8 MUTATED CCDC8 WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC8 MUTATED                                     3
  CCDC8 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC8 MUTATED                                       0
  CCDC8 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC8 MUTATED                                                  0
  CCDC8 WILD-TYPE                                                2
D113V8, multiclass
                                                  clus
vv                                                 CCDC8 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CCDC8 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V9, continuous
[1] "Remove cluster labels:" "CCDC8 MUTATED"         
clus
  CCDC8 MUTATED CCDC8 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"CCDC8 WILD-TYPE" "CCDC8 WILD-TYPE" "CCDC8 WILD-TYPE" "CCDC8 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"CCDC8 WILD-TYPE" "CCDC8 WILD-TYPE" "CCDC8 WILD-TYPE" "CCDC8 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"CCDC8 WILD-TYPE" "CCDC8 WILD-TYPE" 
D113V10, binary
                 cls
clus               0  1
  CCDC8 MUTATED    3  0
  CCDC8 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC8 MUTATED      3    0
  CCDC8 WILD-TYPE   21    9
    clus
vv   CCDC8 MUTATED CCDC8 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D113V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC8 MUTATED       0                         0     3
  CCDC8 WILD-TYPE     2                         3    25
D113V12, multiclass
                           clus
vv                          CCDC8 MUTATED CCDC8 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(114) Variable = HIST1H2BK MUTATION ANALYSIS
D114V1, survival
                     sevent
clus2                  0  1
  HIST1H2BK WILD-TYPE 18  5
HIST1H2BK WILD-TYPE 
                 23 
[1] 5
$`HIST1H2BK WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7652 
          28          361           11           13         1989          476 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
         851           17          329          300         1991            8 
TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
        1968          127          110          416          844 

HIST1H2BK WILD-TYPE 
                  1 
HIST1H2BK WILD-TYPE 
               1991 
HIST1H2BK WILD-TYPE 
                329 
[1] "1.0 - 1991.0 (329.0)"
D114V2, continuous
                     vv
clus                  STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  HIST1H2BK MUTATED          0         0         3         0        0
  HIST1H2BK WILD-TYPE        2         6        20         1        1
D114V3, multiclass
           clus
vv          HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  STAGE IB                  0                   2
  STAGE IIA                 0                   6
  STAGE IIB                 3                  20
  STAGE III                 0                   1
  STAGE IV                  0                   1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                  T2+T3+T4
  HIST1H2BK MUTATED          3
  HIST1H2BK WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D114V5, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    0  3
  HIST1H2BK WILD-TYPE  7 22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      0    3
  HIST1H2BK WILD-TYPE    7   22
   clus
vv  HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  0                 0                   7
  1                 3                  22
[1] 2 2
[1] FALSE
                     vv
clus                  M0 M1 MX
  HIST1H2BK MUTATED    0  0  3
  HIST1H2BK WILD-TYPE 19  1 10
D114V6, multiclass
    clus
vv   HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  M0                 0                  19
  M1                 0                   1
  MX                 3                  10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V7, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    1  2
  HIST1H2BK WILD-TYPE 13 17
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      1    2
  HIST1H2BK WILD-TYPE   13   17
        clus
vv       HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  FEMALE                 1                  13
  MALE                   2                  17
[1] 2 2
[1] FALSE
                     vv
clus                  PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  HIST1H2BK MUTATED                                     2
  HIST1H2BK WILD-TYPE                                  26
                     vv
clus                  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  HIST1H2BK MUTATED                                       1
  HIST1H2BK WILD-TYPE                                     2
                     vv
clus                  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  HIST1H2BK MUTATED                                                  0
  HIST1H2BK WILD-TYPE                                                2
D114V8, multiclass
                                                  clus
vv                                                 HIST1H2BK MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 0
                                                  clus
vv                                                 HIST1H2BK WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                               26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                              2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                   2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V9, continuous
D114V10, binary
                     cls
clus                   0  1
  HIST1H2BK MUTATED    2  1
  HIST1H2BK WILD-TYPE 22  8
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BK MUTATED      2    1
  HIST1H2BK WILD-TYPE   22    8
    clus
vv   HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  R0                 2                  22
  R1                 1                   8
[1] 2 2
[1] FALSE
D114V11, continuous
                     vv
clus                  ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HIST1H2BK MUTATED       0                         0     3
  HIST1H2BK WILD-TYPE     2                         3    25
D114V12, multiclass
                           clus
vv                          HIST1H2BK MUTATED HIST1H2BK WILD-TYPE
  ASIAN                                     0                   2
  BLACK OR AFRICAN AMERICAN                 0                   3
  WHITE                                     3                  25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(115) Variable = SCRIB MUTATION ANALYSIS
D115V1, survival
                 sevent
clus2              0  1
  SCRIB MUTATED    0  1
  SCRIB WILD-TYPE 18  4
  SCRIB MUTATED SCRIB WILD-TYPE 
              1              22 
  SCRIB MUTATED SCRIB WILD-TYPE 
              1               4 
$`SCRIB MUTATED`
TCGA-IB-7651 
        1989 

$`SCRIB WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         127          110          416          844 

  SCRIB MUTATED SCRIB WILD-TYPE 
           1989               1 
  SCRIB MUTATED SCRIB WILD-TYPE 
           1989            1991 
  SCRIB MUTATED SCRIB WILD-TYPE 
         1989.0           314.5 
[1] "1989.0 - 1989.0 (1989.0)" "1.0 - 1991.0 (314.5)"    
[1] "Remove cluster labels:" "SCRIB MUTATED"         
D115V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SCRIB MUTATED          0         0         3         0        0
  SCRIB WILD-TYPE        2         6        20         1        1
D115V3, multiclass
           clus
vv          SCRIB MUTATED SCRIB WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  SCRIB MUTATED          3
  SCRIB WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D115V5, binary
                 cls
clus               0  1
  SCRIB MUTATED    0  3
  SCRIB WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRIB MUTATED      0    3
  SCRIB WILD-TYPE    7   22
   clus
vv  SCRIB MUTATED SCRIB WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  SCRIB MUTATED    1  0  2
  SCRIB WILD-TYPE 18  1 11
D115V6, multiclass
    clus
vv   SCRIB MUTATED SCRIB WILD-TYPE
  M0             1              18
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V7, binary
                 cls
clus               0  1
  SCRIB MUTATED    2  1
  SCRIB WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRIB MUTATED      2    1
  SCRIB WILD-TYPE   12   18
        clus
vv       SCRIB MUTATED SCRIB WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SCRIB MUTATED                                     3
  SCRIB WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SCRIB MUTATED                                       0
  SCRIB WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SCRIB MUTATED                                                  0
  SCRIB WILD-TYPE                                                2
D115V8, multiclass
                                                  clus
vv                                                 SCRIB MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 SCRIB WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V9, continuous
[1] "Remove cluster labels:" "SCRIB MUTATED"         
clus
  SCRIB MUTATED SCRIB WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"SCRIB WILD-TYPE" "SCRIB WILD-TYPE" "SCRIB WILD-TYPE" "SCRIB WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"SCRIB WILD-TYPE" "SCRIB WILD-TYPE" "SCRIB WILD-TYPE" "SCRIB WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"SCRIB WILD-TYPE" "SCRIB WILD-TYPE" 
D115V10, binary
                 cls
clus               0  1
  SCRIB MUTATED    3  0
  SCRIB WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCRIB MUTATED      3    0
  SCRIB WILD-TYPE   21    9
    clus
vv   SCRIB MUTATED SCRIB WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D115V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SCRIB MUTATED       0                         0     3
  SCRIB WILD-TYPE     2                         3    25
D115V12, multiclass
                           clus
vv                          SCRIB MUTATED SCRIB WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(116) Variable = STAU1 MUTATION ANALYSIS
D116V1, survival
                 sevent
clus2              0  1
  STAU1 MUTATED    2  1
  STAU1 WILD-TYPE 16  4
  STAU1 MUTATED STAU1 WILD-TYPE 
              3              20 
  STAU1 MUTATED STAU1 WILD-TYPE 
              1               4 
$`STAU1 MUTATED`
TCGA-IB-7651 TCGA-IB-A5SO TCGA-IB-A5SP 
        1989          329          300 

$`STAU1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
          17         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  STAU1 MUTATED STAU1 WILD-TYPE 
            300               1 
  STAU1 MUTATED STAU1 WILD-TYPE 
           1989            1991 
  STAU1 MUTATED STAU1 WILD-TYPE 
            329             263 
[1] "300.0 - 1989.0 (329.0)" "1.0 - 1991.0 (263.0)"  
[1] "hr=" "1.2"
D116V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  STAU1 MUTATED          0         1         2         0        0
  STAU1 WILD-TYPE        2         5        21         1        1
D116V3, multiclass
           clus
vv          STAU1 MUTATED STAU1 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  STAU1 MUTATED          3
  STAU1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D116V5, binary
                 cls
clus               0  1
  STAU1 MUTATED    1  2
  STAU1 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      1    2
  STAU1 WILD-TYPE    6   23
   clus
vv  STAU1 MUTATED STAU1 WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  STAU1 MUTATED    3  0  0
  STAU1 WILD-TYPE 16  1 13
D116V6, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  M0             3              16
  M1             0               1
  MX             0              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V7, binary
                 cls
clus               0  1
  STAU1 MUTATED    1  2
  STAU1 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      1    2
  STAU1 WILD-TYPE   13   17
        clus
vv       STAU1 MUTATED STAU1 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  STAU1 MUTATED                                     3
  STAU1 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  STAU1 MUTATED                                       0
  STAU1 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  STAU1 MUTATED                                                  0
  STAU1 WILD-TYPE                                                2
D116V8, multiclass
                                                  clus
vv                                                 STAU1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 STAU1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V9, continuous
[1] "Remove cluster labels:" "STAU1 MUTATED"         
clus
  STAU1 MUTATED STAU1 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"STAU1 WILD-TYPE" "STAU1 WILD-TYPE" "STAU1 WILD-TYPE" "STAU1 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"STAU1 WILD-TYPE" "STAU1 WILD-TYPE" "STAU1 WILD-TYPE" "STAU1 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"STAU1 WILD-TYPE" "STAU1 WILD-TYPE" 
D116V10, binary
                 cls
clus               0  1
  STAU1 MUTATED    2  1
  STAU1 WILD-TYPE 22  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      2    1
  STAU1 WILD-TYPE   22    8
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  R0             2              22
  R1             1               8
[1] 2 2
[1] FALSE
D116V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAU1 MUTATED       0                         0     3
  STAU1 WILD-TYPE     2                         3    25
D116V12, multiclass
                           clus
vv                          STAU1 MUTATED STAU1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(117) Variable = GOLGA6B MUTATION ANALYSIS
D117V1, survival
                   sevent
clus2                0  1
  GOLGA6B MUTATED    2  1
  GOLGA6B WILD-TYPE 16  4
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                3                20 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                1                 4 
$`GOLGA6B MUTATED`
TCGA-FB-A78T TCGA-IB-7651 TCGA-US-A776 
           1         1989          844 

$`GOLGA6B WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY 
         110          416 

  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                1                 8 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
             1989              1991 
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
            844.0             314.5 
[1] "1.0 - 1989.0 (844.0)" "8.0 - 1991.0 (314.5)"
[1] "hr=" "1.2"
D117V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GOLGA6B MUTATED          0         1         2         0        0
  GOLGA6B WILD-TYPE        2         5        21         1        1
D117V3, multiclass
           clus
vv          GOLGA6B MUTATED GOLGA6B WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               1                 5
  STAGE IIB               2                21
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  GOLGA6B MUTATED          3
  GOLGA6B WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D117V5, binary
                   cls
clus                 0  1
  GOLGA6B MUTATED    1  2
  GOLGA6B WILD-TYPE  6 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      1    2
  GOLGA6B WILD-TYPE    6   23
   clus
vv  GOLGA6B MUTATED GOLGA6B WILD-TYPE
  0               1                 6
  1               2                23
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  GOLGA6B MUTATED    2  0  1
  GOLGA6B WILD-TYPE 17  1 12
D117V6, multiclass
    clus
vv   GOLGA6B MUTATED GOLGA6B WILD-TYPE
  M0               2                17
  M1               0                 1
  MX               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V7, binary
                   cls
clus                 0  1
  GOLGA6B MUTATED    2  1
  GOLGA6B WILD-TYPE 12 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      2    1
  GOLGA6B WILD-TYPE   12   18
        clus
vv       GOLGA6B MUTATED GOLGA6B WILD-TYPE
  FEMALE               2                12
  MALE                 1                18
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GOLGA6B MUTATED                                     2
  GOLGA6B WILD-TYPE                                  26
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GOLGA6B MUTATED                                       0
  GOLGA6B WILD-TYPE                                     3
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GOLGA6B MUTATED                                                  1
  GOLGA6B WILD-TYPE                                                1
D117V8, multiclass
                                                  clus
vv                                                 GOLGA6B MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 GOLGA6B WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            3
  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"
D117V9, continuous
[1] "Remove cluster labels:" "GOLGA6B MUTATED"       
clus
  GOLGA6B MUTATED GOLGA6B WILD-TYPE 
                2                 9 
       TCGA-FB-A5VM        TCGA-FB-A7DR        TCGA-H8-A6C1        TCGA-IB-7885 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-LB-A7SX 
"GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" "GOLGA6B WILD-TYPE" 
       TCGA-OE-A75W 
"GOLGA6B WILD-TYPE" 
D117V10, binary
                   cls
clus                 0  1
  GOLGA6B MUTATED    3  0
  GOLGA6B WILD-TYPE 21  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLGA6B MUTATED      3    0
  GOLGA6B WILD-TYPE   21    9
    clus
vv   GOLGA6B MUTATED GOLGA6B WILD-TYPE
  R0               3                21
  R1               0                 9
[1] 2 2
[1] FALSE
D117V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GOLGA6B MUTATED       0                         0     3
  GOLGA6B WILD-TYPE     2                         3    25
D117V12, multiclass
                           clus
vv                          GOLGA6B MUTATED GOLGA6B WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   3                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(118) Variable = IRS4 MUTATION ANALYSIS
D118V1, survival
                sevent
clus2             0  1
  IRS4 MUTATED    0  1
  IRS4 WILD-TYPE 18  4
  IRS4 MUTATED IRS4 WILD-TYPE 
             1             22 
  IRS4 MUTATED IRS4 WILD-TYPE 
             1              4 
$`IRS4 MUTATED`
TCGA-IB-7651 
        1989 

$`IRS4 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-LB-A7SX TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         127          110          416          844 

  IRS4 MUTATED IRS4 WILD-TYPE 
          1989              1 
  IRS4 MUTATED IRS4 WILD-TYPE 
          1989           1991 
  IRS4 MUTATED IRS4 WILD-TYPE 
        1989.0          314.5 
[1] "1989.0 - 1989.0 (1989.0)" "1.0 - 1991.0 (314.5)"    
[1] "Remove cluster labels:" "IRS4 MUTATED"          
D118V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  IRS4 MUTATED          0         0         3         0        0
  IRS4 WILD-TYPE        2         6        20         1        1
D118V3, multiclass
           clus
vv          IRS4 MUTATED IRS4 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            0              6
  STAGE IIB            3             20
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  IRS4 MUTATED          3
  IRS4 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D118V5, binary
                cls
clus              0  1
  IRS4 MUTATED    0  3
  IRS4 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      0    3
  IRS4 WILD-TYPE    7   22
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  IRS4 MUTATED    1  0  2
  IRS4 WILD-TYPE 18  1 11
D118V6, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  M0            1             18
  M1            0              1
  MX            2             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V7, binary
                cls
clus              0  1
  IRS4 MUTATED    2  1
  IRS4 WILD-TYPE 12 18
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      2    1
  IRS4 WILD-TYPE   12   18
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE            2             12
  MALE              1             18
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  IRS4 MUTATED                                     3
  IRS4 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  IRS4 MUTATED                                       0
  IRS4 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  IRS4 MUTATED                                                  0
  IRS4 WILD-TYPE                                                2
D118V8, multiclass
                                                  clus
vv                                                 IRS4 MUTATED IRS4 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              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"
D118V9, continuous
[1] "Remove cluster labels:" "IRS4 MUTATED"          
clus
  IRS4 MUTATED IRS4 WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"IRS4 WILD-TYPE" "IRS4 WILD-TYPE" 
D118V10, binary
                cls
clus              0  1
  IRS4 MUTATED    3  0
  IRS4 WILD-TYPE 21  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED      3    0
  IRS4 WILD-TYPE   21    9
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  R0            3             21
  R1            0              9
[1] 2 2
[1] FALSE
D118V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED       0                         0     3
  IRS4 WILD-TYPE     2                         3    25
D118V12, multiclass
                           clus
vv                          IRS4 MUTATED IRS4 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(119) Variable = PDZD2 MUTATION ANALYSIS
D119V1, survival
                 sevent
clus2              0  1
  PDZD2 MUTATED    2  1
  PDZD2 WILD-TYPE 16  4
  PDZD2 MUTATED PDZD2 WILD-TYPE 
              3              20 
  PDZD2 MUTATED PDZD2 WILD-TYPE 
              1               4 
$`PDZD2 MUTATED`
TCGA-IB-7651 TCGA-IB-7652 TCGA-OE-A75W 
        1989          476          110 

$`PDZD2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7885 TCGA-IB-8126 
          28          361           11           13          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  PDZD2 MUTATED PDZD2 WILD-TYPE 
            110               1 
  PDZD2 MUTATED PDZD2 WILD-TYPE 
           1989            1991 
  PDZD2 MUTATED PDZD2 WILD-TYPE 
          476.0           314.5 
[1] "110.0 - 1989.0 (476.0)" "1.0 - 1991.0 (314.5)"  
[1] "hr=" "1.2"
D119V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PDZD2 MUTATED          1         1         2         0        0
  PDZD2 WILD-TYPE        1         5        21         1        1
D119V3, multiclass
           clus
vv          PDZD2 MUTATED PDZD2 WILD-TYPE
  STAGE IB              1               1
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  PDZD2 MUTATED          4
  PDZD2 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D119V5, binary
                 cls
clus               0  1
  PDZD2 MUTATED    2  2
  PDZD2 WILD-TYPE  5 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD2 MUTATED      2    2
  PDZD2 WILD-TYPE    5   23
   clus
vv  PDZD2 MUTATED PDZD2 WILD-TYPE
  0             2               5
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  PDZD2 MUTATED    4  0  0
  PDZD2 WILD-TYPE 15  1 13
D119V6, multiclass
    clus
vv   PDZD2 MUTATED PDZD2 WILD-TYPE
  M0             4              15
  M1             0               1
  MX             0              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V7, binary
                 cls
clus               0  1
  PDZD2 MUTATED    3  1
  PDZD2 WILD-TYPE 11 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD2 MUTATED      3    1
  PDZD2 WILD-TYPE   11   18
        clus
vv       PDZD2 MUTATED PDZD2 WILD-TYPE
  FEMALE             3              11
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PDZD2 MUTATED                                     4
  PDZD2 WILD-TYPE                                  24
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PDZD2 MUTATED                                       0
  PDZD2 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PDZD2 MUTATED                                                  0
  PDZD2 WILD-TYPE                                                2
D119V8, multiclass
                                                  clus
vv                                                 PDZD2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 PDZD2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V9, continuous
[1] "Remove cluster labels:" "PDZD2 MUTATED"         
clus
  PDZD2 MUTATED PDZD2 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"PDZD2 WILD-TYPE" "PDZD2 WILD-TYPE" "PDZD2 WILD-TYPE" "PDZD2 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"PDZD2 WILD-TYPE" "PDZD2 WILD-TYPE" "PDZD2 WILD-TYPE" "PDZD2 WILD-TYPE" 
     TCGA-LB-A7SX 
"PDZD2 WILD-TYPE" 
D119V10, binary
                 cls
clus               0  1
  PDZD2 MUTATED    3  1
  PDZD2 WILD-TYPE 21  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD2 MUTATED      3    1
  PDZD2 WILD-TYPE   21    8
    clus
vv   PDZD2 MUTATED PDZD2 WILD-TYPE
  R0             3              21
  R1             1               8
[1] 2 2
[1] FALSE
D119V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PDZD2 MUTATED       1                         0     3
  PDZD2 WILD-TYPE     1                         3    25
D119V12, multiclass
                           clus
vv                          PDZD2 MUTATED PDZD2 WILD-TYPE
  ASIAN                                 1               1
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(120) Variable = CCDC135 MUTATION ANALYSIS
D120V1, survival
                   sevent
clus2                0  1
  CCDC135 MUTATED    2  1
  CCDC135 WILD-TYPE 16  4
  CCDC135 MUTATED CCDC135 WILD-TYPE 
                3                20 
  CCDC135 MUTATED CCDC135 WILD-TYPE 
                1                 4 
$`CCDC135 MUTATED`
TCGA-HZ-A77P TCGA-IB-7651 TCGA-US-A776 
          13         1989          844 

$`CCDC135 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
          28          361           11          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY 
         110          416 

  CCDC135 MUTATED CCDC135 WILD-TYPE 
               13                 1 
  CCDC135 MUTATED CCDC135 WILD-TYPE 
             1989              1991 
  CCDC135 MUTATED CCDC135 WILD-TYPE 
            844.0             314.5 
[1] "13.0 - 1989.0 (844.0)" "1.0 - 1991.0 (314.5)" 
[1] "hr=" "1.2"
D120V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CCDC135 MUTATED          0         1         2         0        0
  CCDC135 WILD-TYPE        2         5        21         1        1
D120V3, multiclass
           clus
vv          CCDC135 MUTATED CCDC135 WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               1                 5
  STAGE IIB               2                21
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  CCDC135 MUTATED          3
  CCDC135 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D120V5, binary
                   cls
clus                 0  1
  CCDC135 MUTATED    1  2
  CCDC135 WILD-TYPE  6 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC135 MUTATED      1    2
  CCDC135 WILD-TYPE    6   23
   clus
vv  CCDC135 MUTATED CCDC135 WILD-TYPE
  0               1                 6
  1               2                23
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  CCDC135 MUTATED    1  0  2
  CCDC135 WILD-TYPE 18  1 11
D120V6, multiclass
    clus
vv   CCDC135 MUTATED CCDC135 WILD-TYPE
  M0               1                18
  M1               0                 1
  MX               2                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V7, binary
                   cls
clus                 0  1
  CCDC135 MUTATED    1  2
  CCDC135 WILD-TYPE 13 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC135 MUTATED      1    2
  CCDC135 WILD-TYPE   13   17
        clus
vv       CCDC135 MUTATED CCDC135 WILD-TYPE
  FEMALE               1                13
  MALE                 2                17
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CCDC135 MUTATED                                     1
  CCDC135 WILD-TYPE                                  27
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CCDC135 MUTATED                                       1
  CCDC135 WILD-TYPE                                     2
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CCDC135 MUTATED                                                  1
  CCDC135 WILD-TYPE                                                1
D120V8, multiclass
                                                  clus
vv                                                 CCDC135 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            1
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 CCDC135 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             27
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            2
  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"
D120V9, continuous
[1] "Remove cluster labels:" "CCDC135 MUTATED"       
clus
  CCDC135 MUTATED CCDC135 WILD-TYPE 
                1                10 
       TCGA-FB-A5VM        TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-H8-A6C1 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W 
"CCDC135 WILD-TYPE" "CCDC135 WILD-TYPE" 
D120V10, binary
                   cls
clus                 0  1
  CCDC135 MUTATED    3  0
  CCDC135 WILD-TYPE 21  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC135 MUTATED      3    0
  CCDC135 WILD-TYPE   21    9
    clus
vv   CCDC135 MUTATED CCDC135 WILD-TYPE
  R0               3                21
  R1               0                 9
[1] 2 2
[1] FALSE
D120V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC135 MUTATED       0                         0     3
  CCDC135 WILD-TYPE     2                         3    25
D120V12, multiclass
                           clus
vv                          CCDC135 MUTATED CCDC135 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   3                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(121) Variable = CEP72 MUTATION ANALYSIS
D121V1, survival
                 sevent
clus2              0  1
  CEP72 MUTATED    2  1
  CEP72 WILD-TYPE 16  4
  CEP72 MUTATED CEP72 WILD-TYPE 
              3              20 
  CEP72 MUTATED CEP72 WILD-TYPE 
              1               4 
$`CEP72 MUTATED`
TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-IB-7651 
         396          361         1989 

$`CEP72 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7918 
         360          153          449            1          166           28 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO 
          11           13          476          851           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  CEP72 MUTATED CEP72 WILD-TYPE 
            361               1 
  CEP72 MUTATED CEP72 WILD-TYPE 
           1989            1991 
  CEP72 MUTATED CEP72 WILD-TYPE 
            396             233 
[1] "361.0 - 1989.0 (396.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.5"
D121V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  CEP72 MUTATED          0         1         2         0        0
  CEP72 WILD-TYPE        2         5        21         1        1
D121V3, multiclass
           clus
vv          CEP72 MUTATED CEP72 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             1               5
  STAGE IIB             2              21
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  CEP72 MUTATED          3
  CEP72 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D121V5, binary
                 cls
clus               0  1
  CEP72 MUTATED    1  2
  CEP72 WILD-TYPE  6 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP72 MUTATED      1    2
  CEP72 WILD-TYPE    6   23
   clus
vv  CEP72 MUTATED CEP72 WILD-TYPE
  0             1               6
  1             2              23
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  CEP72 MUTATED    1  0  2
  CEP72 WILD-TYPE 18  1 11
D121V6, multiclass
    clus
vv   CEP72 MUTATED CEP72 WILD-TYPE
  M0             1              18
  M1             0               1
  MX             2              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V7, binary
                 cls
clus               0  1
  CEP72 MUTATED    1  2
  CEP72 WILD-TYPE 13 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP72 MUTATED      1    2
  CEP72 WILD-TYPE   13   17
        clus
vv       CEP72 MUTATED CEP72 WILD-TYPE
  FEMALE             1              13
  MALE               2              17
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  CEP72 MUTATED                                     2
  CEP72 WILD-TYPE                                  26
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  CEP72 MUTATED                                       1
  CEP72 WILD-TYPE                                     2
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  CEP72 MUTATED                                                  0
  CEP72 WILD-TYPE                                                2
D121V8, multiclass
                                                  clus
vv                                                 CEP72 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 CEP72 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V9, continuous
[1] "Remove cluster labels:" "CEP72 MUTATED"         
clus
  CEP72 MUTATED CEP72 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-IB-7885 
"CEP72 WILD-TYPE" "CEP72 WILD-TYPE" "CEP72 WILD-TYPE" "CEP72 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"CEP72 WILD-TYPE" "CEP72 WILD-TYPE" "CEP72 WILD-TYPE" "CEP72 WILD-TYPE" 
     TCGA-OE-A75W 
"CEP72 WILD-TYPE" 
D121V10, binary
                 cls
clus               0  1
  CEP72 MUTATED    3  0
  CEP72 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEP72 MUTATED      3    0
  CEP72 WILD-TYPE   21    9
    clus
vv   CEP72 MUTATED CEP72 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D121V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEP72 MUTATED       0                         0     3
  CEP72 WILD-TYPE     2                         3    25
D121V12, multiclass
                           clus
vv                          CEP72 MUTATED CEP72 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(122) Variable = SMARCA2 MUTATION ANALYSIS
D122V1, survival
                   sevent
clus2                0  1
  SMARCA2 MUTATED    1  1
  SMARCA2 WILD-TYPE 17  4
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                2                21 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                1                 4 
$`SMARCA2 MUTATED`
TCGA-FB-A5VM TCGA-IB-7651 
         449         1989 

$`SMARCA2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
              449                 1 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
             1989              1991 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
             1219               300 
[1] "449.0 - 1989.0 (1219.0)" "1.0 - 1991.0 (300.0)"   
[1] "Remove cluster labels:" "SMARCA2 MUTATED"       
D122V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  SMARCA2 MUTATED          1         0         2         0        0
  SMARCA2 WILD-TYPE        1         6        21         1        1
D122V3, multiclass
           clus
vv          SMARCA2 MUTATED SMARCA2 WILD-TYPE
  STAGE IB                1                 1
  STAGE IIA               0                 6
  STAGE IIB               2                21
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  SMARCA2 MUTATED          3
  SMARCA2 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D122V5, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    1  2
  SMARCA2 WILD-TYPE  6 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      1    2
  SMARCA2 WILD-TYPE    6   23
   clus
vv  SMARCA2 MUTATED SMARCA2 WILD-TYPE
  0               1                 6
  1               2                23
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  SMARCA2 MUTATED    2  0  1
  SMARCA2 WILD-TYPE 17  1 12
D122V6, multiclass
    clus
vv   SMARCA2 MUTATED SMARCA2 WILD-TYPE
  M0               2                17
  M1               0                 1
  MX               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V7, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    2  1
  SMARCA2 WILD-TYPE 12 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      2    1
  SMARCA2 WILD-TYPE   12   18
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  FEMALE               2                12
  MALE                 1                18
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  SMARCA2 MUTATED                                     3
  SMARCA2 WILD-TYPE                                  25
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  SMARCA2 MUTATED                                       0
  SMARCA2 WILD-TYPE                                     3
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  SMARCA2 MUTATED                                                  0
  SMARCA2 WILD-TYPE                                                2
D122V8, multiclass
                                                  clus
vv                                                 SMARCA2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 SMARCA2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V9, continuous
[1] "Remove cluster labels:" "SMARCA2 MUTATED"       
clus
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                2                 9 
       TCGA-FB-A78T        TCGA-FB-A7DR        TCGA-H8-A6C1        TCGA-IB-7885 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-LB-A7SX 
"SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" "SMARCA2 WILD-TYPE" 
       TCGA-OE-A75W 
"SMARCA2 WILD-TYPE" 
D122V10, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    3  0
  SMARCA2 WILD-TYPE 21  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      3    0
  SMARCA2 WILD-TYPE   21    9
    clus
vv   SMARCA2 MUTATED SMARCA2 WILD-TYPE
  R0               3                21
  R1               0                 9
[1] 2 2
[1] FALSE
D122V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMARCA2 MUTATED       0                         0     3
  SMARCA2 WILD-TYPE     2                         3    25
D122V12, multiclass
                           clus
vv                          SMARCA2 MUTATED SMARCA2 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   3                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(123) Variable = UBXN6 MUTATION ANALYSIS
D123V1, survival
                 sevent
clus2              0  1
  UBXN6 MUTATED    0  2
  UBXN6 WILD-TYPE 18  3
  UBXN6 MUTATED UBXN6 WILD-TYPE 
              2              21 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
              2               3 
$`UBXN6 MUTATED`
TCGA-F2-A44G TCGA-IB-7651 
         153         1989 

$`UBXN6 WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  UBXN6 MUTATED UBXN6 WILD-TYPE 
            153               1 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
           1989            1991 
  UBXN6 MUTATED UBXN6 WILD-TYPE 
           1071             329 
[1] "153.0 - 1989.0 (1071.0)" "1.0 - 1991.0 (329.0)"   
[1] "Remove cluster labels:" "UBXN6 MUTATED"         
D123V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  UBXN6 MUTATED          0         0         3         0        0
  UBXN6 WILD-TYPE        2         6        20         1        1
D123V3, multiclass
           clus
vv          UBXN6 MUTATED UBXN6 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  UBXN6 MUTATED          3
  UBXN6 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D123V5, binary
                 cls
clus               0  1
  UBXN6 MUTATED    0  3
  UBXN6 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      0    3
  UBXN6 WILD-TYPE    7   22
   clus
vv  UBXN6 MUTATED UBXN6 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  UBXN6 MUTATED    2  0  1
  UBXN6 WILD-TYPE 17  1 12
D123V6, multiclass
    clus
vv   UBXN6 MUTATED UBXN6 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V7, binary
                 cls
clus               0  1
  UBXN6 MUTATED    2  1
  UBXN6 WILD-TYPE 12 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      2    1
  UBXN6 WILD-TYPE   12   18
        clus
vv       UBXN6 MUTATED UBXN6 WILD-TYPE
  FEMALE             2              12
  MALE               1              18
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  UBXN6 MUTATED                                     3
  UBXN6 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  UBXN6 MUTATED                                       0
  UBXN6 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  UBXN6 MUTATED                                                  0
  UBXN6 WILD-TYPE                                                2
D123V8, multiclass
                                                  clus
vv                                                 UBXN6 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 UBXN6 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V9, continuous
[1] "Remove cluster labels:" "UBXN6 MUTATED"         
clus
  UBXN6 MUTATED UBXN6 WILD-TYPE 
              1              10 
     TCGA-FB-A5VM      TCGA-FB-A78T      TCGA-FB-A7DR      TCGA-H8-A6C1 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-IB-7885      TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
     TCGA-LB-A7SX      TCGA-OE-A75W 
"UBXN6 WILD-TYPE" "UBXN6 WILD-TYPE" 
D123V10, binary
                 cls
clus               0  1
  UBXN6 MUTATED    1  2
  UBXN6 WILD-TYPE 23  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBXN6 MUTATED      1    2
  UBXN6 WILD-TYPE   23    7
    clus
vv   UBXN6 MUTATED UBXN6 WILD-TYPE
  R0             1              23
  R1             2               7
[1] 2 2
[1] FALSE
D123V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  UBXN6 MUTATED       0                         0     3
  UBXN6 WILD-TYPE     2                         3    25
D123V12, multiclass
                           clus
vv                          UBXN6 MUTATED UBXN6 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(124) Variable = YIPF2 MUTATION ANALYSIS
D124V1, survival
                 sevent
clus2              0  1
  YIPF2 MUTATED    1  1
  YIPF2 WILD-TYPE 17  4
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              2              21 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              1               4 
$`YIPF2 MUTATED`
TCGA-FB-A78T TCGA-IB-7651 
           1         1989 

$`YIPF2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  YIPF2 MUTATED YIPF2 WILD-TYPE 
              1               8 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
           1989            1991 
  YIPF2 MUTATED YIPF2 WILD-TYPE 
            995             329 
[1] "1.0 - 1989.0 (995.0)" "8.0 - 1991.0 (329.0)"
[1] "Remove cluster labels:" "YIPF2 MUTATED"         
D124V2, continuous
                 vv
clus              STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  YIPF2 MUTATED          0         0         3         0        0
  YIPF2 WILD-TYPE        2         6        20         1        1
D124V3, multiclass
           clus
vv          YIPF2 MUTATED YIPF2 WILD-TYPE
  STAGE IB              0               2
  STAGE IIA             0               6
  STAGE IIB             3              20
  STAGE III             0               1
  STAGE IV              0               1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T2+T3+T4
  YIPF2 MUTATED          3
  YIPF2 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D124V5, binary
                 cls
clus               0  1
  YIPF2 MUTATED    0  3
  YIPF2 WILD-TYPE  7 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      0    3
  YIPF2 WILD-TYPE    7   22
   clus
vv  YIPF2 MUTATED YIPF2 WILD-TYPE
  0             0               7
  1             3              22
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  YIPF2 MUTATED    2  0  1
  YIPF2 WILD-TYPE 17  1 12
D124V6, multiclass
    clus
vv   YIPF2 MUTATED YIPF2 WILD-TYPE
  M0             2              17
  M1             0               1
  MX             1              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V7, binary
                 cls
clus               0  1
  YIPF2 MUTATED    3  0
  YIPF2 WILD-TYPE 11 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      3    0
  YIPF2 WILD-TYPE   11   19
        clus
vv       YIPF2 MUTATED YIPF2 WILD-TYPE
  FEMALE             3              11
  MALE               0              19
[1] 2 2
[1] FALSE
                 vv
clus              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  YIPF2 MUTATED                                     3
  YIPF2 WILD-TYPE                                  25
                 vv
clus              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  YIPF2 MUTATED                                       0
  YIPF2 WILD-TYPE                                     3
                 vv
clus              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  YIPF2 MUTATED                                                  0
  YIPF2 WILD-TYPE                                                2
D124V8, multiclass
                                                  clus
vv                                                 YIPF2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                          3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA             0
                                                  clus
vv                                                 YIPF2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V9, continuous
[1] "Remove cluster labels:" "YIPF2 MUTATED"         
clus
  YIPF2 MUTATED YIPF2 WILD-TYPE 
              2               9 
     TCGA-FB-A5VM      TCGA-FB-A7DR      TCGA-H8-A6C1      TCGA-IB-7885 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-IB-8126      TCGA-IB-A5SS      TCGA-IB-A6UG      TCGA-LB-A7SX 
"YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" "YIPF2 WILD-TYPE" 
     TCGA-OE-A75W 
"YIPF2 WILD-TYPE" 
D124V10, binary
                 cls
clus               0  1
  YIPF2 MUTATED    3  0
  YIPF2 WILD-TYPE 21  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF2 MUTATED      3    0
  YIPF2 WILD-TYPE   21    9
    clus
vv   YIPF2 MUTATED YIPF2 WILD-TYPE
  R0             3              21
  R1             0               9
[1] 2 2
[1] FALSE
D124V11, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  YIPF2 MUTATED       0                         0     3
  YIPF2 WILD-TYPE     2                         3    25
D124V12, multiclass
                           clus
vv                          YIPF2 MUTATED YIPF2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               3
  WHITE                                 3              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(125) Variable = GNAS MUTATION ANALYSIS
D125V1, survival
                sevent
clus2             0  1
  GNAS MUTATED    2  2
  GNAS WILD-TYPE 16  3
  GNAS MUTATED GNAS WILD-TYPE 
             4             19 
  GNAS MUTATED GNAS WILD-TYPE 
             2              3 
$`GNAS MUTATED`
TCGA-F2-A44G TCGA-IB-7651 TCGA-IB-A5SO TCGA-US-A776 
         153         1989          329          844 

$`GNAS WILD-TYPE`
TCGA-F2-7273 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          449            1          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY 
         416 

  GNAS MUTATED GNAS WILD-TYPE 
           153              1 
  GNAS MUTATED GNAS WILD-TYPE 
          1989           1991 
  GNAS MUTATED GNAS WILD-TYPE 
         586.5          300.0 
[1] "153.0 - 1989.0 (586.5)" "1.0 - 1991.0 (300.0)"  
[1] "hr=" "2.2"
D125V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  GNAS MUTATED          0         1         4         0        0
  GNAS WILD-TYPE        2         5        19         1        1
D125V3, multiclass
           clus
vv          GNAS MUTATED GNAS WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            1              5
  STAGE IIB            4             19
  STAGE III            0              1
  STAGE IV             0              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  GNAS MUTATED          5
  GNAS WILD-TYPE       28
[1] "NOT AVAILABLE: table dimension [2x1]"
D125V5, binary
                cls
clus              0  1
  GNAS MUTATED    1  4
  GNAS WILD-TYPE  6 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      1    4
  GNAS WILD-TYPE    6   21
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            1              6
  1            4             21
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  GNAS MUTATED    3  0  2
  GNAS WILD-TYPE 16  1 11
D125V6, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  M0            3             16
  M1            0              1
  MX            2             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V7, binary
                cls
clus              0  1
  GNAS MUTATED    2  3
  GNAS WILD-TYPE 12 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      2    3
  GNAS WILD-TYPE   12   16
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE            2             12
  MALE              3             16
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  GNAS MUTATED                                     3
  GNAS WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  GNAS MUTATED                                       1
  GNAS WILD-TYPE                                     2
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  GNAS MUTATED                                                  1
  GNAS WILD-TYPE                                                1
D125V8, multiclass
                                                  clus
vv                                                 GNAS MUTATED GNAS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       1              2
  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"
D125V9, continuous
[1] "Remove cluster labels:" "GNAS MUTATED"          
clus
  GNAS MUTATED GNAS WILD-TYPE 
             1             10 
    TCGA-FB-A5VM     TCGA-FB-A78T     TCGA-FB-A7DR     TCGA-H8-A6C1 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-IB-7885     TCGA-IB-8126     TCGA-IB-A5SS     TCGA-IB-A6UG 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" "GNAS WILD-TYPE" 
    TCGA-LB-A7SX     TCGA-OE-A75W 
"GNAS WILD-TYPE" "GNAS WILD-TYPE" 
D125V10, binary
                cls
clus              0  1
  GNAS MUTATED    3  2
  GNAS WILD-TYPE 21  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      3    2
  GNAS WILD-TYPE   21    7
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0            3             21
  R1            2              7
[1] 2 2
[1] FALSE
D125V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GNAS MUTATED       0                         0     5
  GNAS WILD-TYPE     2                         3    23
D125V12, multiclass
                           clus
vv                          GNAS MUTATED GNAS WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                5             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(126) Variable = TGFBR2 MUTATION ANALYSIS
D126V1, survival
                  sevent
clus2               0  1
  TGFBR2 MUTATED    2  1
  TGFBR2 WILD-TYPE 16  4
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               3               20 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               1                4 
$`TGFBR2 MUTATED`
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-A5SO 
        1989          851          329 

$`TGFBR2 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 
          28          361           11           13          476           17 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
             329                1 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            1989             1991 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
             851              233 
[1] "329.0 - 1989.0 (851.0)" "1.0 - 1991.0 (233.0)"  
[1] "hr=" "1.3"
D126V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TGFBR2 MUTATED          0         0         3         0        0
  TGFBR2 WILD-TYPE        2         6        20         1        1
D126V3, multiclass
           clus
vv          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              0                6
  STAGE IIB              3               20
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  TGFBR2 MUTATED          3
  TGFBR2 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D126V5, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    0  3
  TGFBR2 WILD-TYPE  7 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      0    3
  TGFBR2 WILD-TYPE    7   22
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0              0                7
  1              3               22
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  TGFBR2 MUTATED    3  0  0
  TGFBR2 WILD-TYPE 16  1 13
D126V6, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  M0              3               16
  M1              0                1
  MX              0               13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V7, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    2  1
  TGFBR2 WILD-TYPE 12 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      2    1
  TGFBR2 WILD-TYPE   12   18
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE              2               12
  MALE                1               18
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TGFBR2 MUTATED                                     3
  TGFBR2 WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TGFBR2 MUTATED                                       0
  TGFBR2 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TGFBR2 MUTATED                                                  0
  TGFBR2 WILD-TYPE                                                2
D126V8, multiclass
                                                  clus
vv                                                 TGFBR2 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 TGFBR2 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V9, continuous
[1] "Remove cluster labels:" "TGFBR2 MUTATED"        
clus
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-H8-A6C1 
"TGFBR2 WILD-TYPE" "TGFBR2 WILD-TYPE" "TGFBR2 WILD-TYPE" "TGFBR2 WILD-TYPE" 
      TCGA-IB-8126       TCGA-IB-A5SS       TCGA-IB-A6UG       TCGA-LB-A7SX 
"TGFBR2 WILD-TYPE" "TGFBR2 WILD-TYPE" "TGFBR2 WILD-TYPE" "TGFBR2 WILD-TYPE" 
      TCGA-OE-A75W 
"TGFBR2 WILD-TYPE" 
D126V10, binary
                  cls
clus                0  1
  TGFBR2 MUTATED    3  0
  TGFBR2 WILD-TYPE 21  9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED      3    0
  TGFBR2 WILD-TYPE   21    9
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  R0              3               21
  R1              0                9
[1] 2 2
[1] FALSE
D126V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED       0                         0     3
  TGFBR2 WILD-TYPE     2                         3    25
D126V12, multiclass
                           clus
vv                          TGFBR2 MUTATED TGFBR2 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(127) Variable = PTPN21 MUTATION ANALYSIS
D127V1, survival
                  sevent
clus2               0  1
  PTPN21 MUTATED    1  2
  PTPN21 WILD-TYPE 17  3
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               3               20 
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               2                3 
$`PTPN21 MUTATED`
TCGA-IB-7651 TCGA-IB-A5SP TCGA-IB-A6UG 
        1989          300         1968 

$`PTPN21 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-LB-A7SX TCGA-OE-A75W 
          17          329         1991            8          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  PTPN21 MUTATED PTPN21 WILD-TYPE 
             300                1 
  PTPN21 MUTATED PTPN21 WILD-TYPE 
            1989             1991 
  PTPN21 MUTATED PTPN21 WILD-TYPE 
          1968.0            247.5 
[1] "300.0 - 1989.0 (1968.0)" "1.0 - 1991.0 (247.5)"   
[1] "hr=" "1.8"
D127V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  PTPN21 MUTATED          0         1         2         0        0
  PTPN21 WILD-TYPE        2         5        21         1        1
D127V3, multiclass
           clus
vv          PTPN21 MUTATED PTPN21 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              1                5
  STAGE IIB              2               21
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  PTPN21 MUTATED          3
  PTPN21 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D127V5, binary
                  cls
clus                0  1
  PTPN21 MUTATED    1  2
  PTPN21 WILD-TYPE  6 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN21 MUTATED      1    2
  PTPN21 WILD-TYPE    6   23
   clus
vv  PTPN21 MUTATED PTPN21 WILD-TYPE
  0              1                6
  1              2               23
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  PTPN21 MUTATED    3  0  0
  PTPN21 WILD-TYPE 16  1 13
D127V6, multiclass
    clus
vv   PTPN21 MUTATED PTPN21 WILD-TYPE
  M0              3               16
  M1              0                1
  MX              0               13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V7, binary
                  cls
clus                0  1
  PTPN21 MUTATED    1  2
  PTPN21 WILD-TYPE 13 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN21 MUTATED      1    2
  PTPN21 WILD-TYPE   13   17
        clus
vv       PTPN21 MUTATED PTPN21 WILD-TYPE
  FEMALE              1               13
  MALE                2               17
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  PTPN21 MUTATED                                     3
  PTPN21 WILD-TYPE                                  25
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  PTPN21 MUTATED                                       0
  PTPN21 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  PTPN21 MUTATED                                                  0
  PTPN21 WILD-TYPE                                                2
D127V8, multiclass
                                                  clus
vv                                                 PTPN21 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 PTPN21 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V9, continuous
[1] "Remove cluster labels:" "PTPN21 MUTATED"        
clus
  PTPN21 MUTATED PTPN21 WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-H8-A6C1 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A5SS       TCGA-LB-A7SX 
"PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" "PTPN21 WILD-TYPE" 
      TCGA-OE-A75W 
"PTPN21 WILD-TYPE" 
D127V10, binary
                  cls
clus                0  1
  PTPN21 MUTATED    1  2
  PTPN21 WILD-TYPE 23  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN21 MUTATED      1    2
  PTPN21 WILD-TYPE   23    7
    clus
vv   PTPN21 MUTATED PTPN21 WILD-TYPE
  R0              1               23
  R1              2                7
[1] 2 2
[1] FALSE
D127V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTPN21 MUTATED       0                         0     3
  PTPN21 WILD-TYPE     2                         3    25
D127V12, multiclass
                           clus
vv                          PTPN21 MUTATED PTPN21 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  3               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(128) Variable = TSC22D1 MUTATION ANALYSIS
D128V1, survival
                   sevent
clus2                0  1
  TSC22D1 MUTATED    2  1
  TSC22D1 WILD-TYPE 16  4
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                3                20 
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                1                 4 
$`TSC22D1 MUTATED`
TCGA-FB-A78T TCGA-IB-7651 TCGA-US-A776 
           1         1989          844 

$`TSC22D1 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449          166          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 
         361           11           13          476          851           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX 
         329          300         1991            8         1968          127 
TCGA-OE-A75W TCGA-Q3-A5QY 
         110          416 

  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                1                 8 
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
             1989              1991 
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
            844.0             314.5 
[1] "1.0 - 1989.0 (844.0)" "8.0 - 1991.0 (314.5)"
[1] "hr=" "1.2"
D128V2, continuous
                   vv
clus                STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  TSC22D1 MUTATED          0         1         2         0        0
  TSC22D1 WILD-TYPE        2         5        21         1        1
D128V3, multiclass
           clus
vv          TSC22D1 MUTATED TSC22D1 WILD-TYPE
  STAGE IB                0                 2
  STAGE IIA               1                 5
  STAGE IIB               2                21
  STAGE III               0                 1
  STAGE IV                0                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T2+T3+T4
  TSC22D1 MUTATED          3
  TSC22D1 WILD-TYPE       30
[1] "NOT AVAILABLE: table dimension [2x1]"
D128V5, binary
                   cls
clus                 0  1
  TSC22D1 MUTATED    1  2
  TSC22D1 WILD-TYPE  6 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D1 MUTATED      1    2
  TSC22D1 WILD-TYPE    6   23
   clus
vv  TSC22D1 MUTATED TSC22D1 WILD-TYPE
  0               1                 6
  1               2                23
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  TSC22D1 MUTATED    2  0  1
  TSC22D1 WILD-TYPE 17  1 12
D128V6, multiclass
    clus
vv   TSC22D1 MUTATED TSC22D1 WILD-TYPE
  M0               2                17
  M1               0                 1
  MX               1                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V7, binary
                   cls
clus                 0  1
  TSC22D1 MUTATED    2  1
  TSC22D1 WILD-TYPE 12 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D1 MUTATED      2    1
  TSC22D1 WILD-TYPE   12   18
        clus
vv       TSC22D1 MUTATED TSC22D1 WILD-TYPE
  FEMALE               2                12
  MALE                 1                18
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  TSC22D1 MUTATED                                     2
  TSC22D1 WILD-TYPE                                  26
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  TSC22D1 MUTATED                                       0
  TSC22D1 WILD-TYPE                                     3
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  TSC22D1 MUTATED                                                  1
  TSC22D1 WILD-TYPE                                                1
D128V8, multiclass
                                                  clus
vv                                                 TSC22D1 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 TSC22D1 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            3
  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"
D128V9, continuous
[1] "Remove cluster labels:" "TSC22D1 MUTATED"       
clus
  TSC22D1 MUTATED TSC22D1 WILD-TYPE 
                2                 9 
       TCGA-FB-A5VM        TCGA-FB-A7DR        TCGA-H8-A6C1        TCGA-IB-7885 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-LB-A7SX 
"TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" "TSC22D1 WILD-TYPE" 
       TCGA-OE-A75W 
"TSC22D1 WILD-TYPE" 
D128V10, binary
                   cls
clus                 0  1
  TSC22D1 MUTATED    3  0
  TSC22D1 WILD-TYPE 21  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TSC22D1 MUTATED      3    0
  TSC22D1 WILD-TYPE   21    9
    clus
vv   TSC22D1 MUTATED TSC22D1 WILD-TYPE
  R0               3                21
  R1               0                 9
[1] 2 2
[1] FALSE
D128V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TSC22D1 MUTATED       0                         0     3
  TSC22D1 WILD-TYPE     2                         3    25
D128V12, multiclass
                           clus
vv                          TSC22D1 MUTATED TSC22D1 WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   3                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(129) Variable = ZNF184 MUTATION ANALYSIS
D129V1, survival
                  sevent
clus2               0  1
  ZNF184 MUTATED    0  2
  ZNF184 WILD-TYPE 18  3
  ZNF184 MUTATED ZNF184 WILD-TYPE 
               2               21 
  ZNF184 MUTATED ZNF184 WILD-TYPE 
               2                3 
$`ZNF184 MUTATED`
TCGA-IB-7651 TCGA-IB-A6UG 
        1989         1968 

$`ZNF184 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 
         360          153          449            1          166          396 
TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7885 
          28          361           11           13          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-LB-A7SX 
          17          329          300         1991            8          127 
TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A776 
         110          416          844 

  ZNF184 MUTATED ZNF184 WILD-TYPE 
            1968                1 
  ZNF184 MUTATED ZNF184 WILD-TYPE 
            1989             1991 
  ZNF184 MUTATED ZNF184 WILD-TYPE 
          1978.5            300.0 
[1] "1968.0 - 1989.0 (1978.5)" "1.0 - 1991.0 (300.0)"    
[1] "Remove cluster labels:" "ZNF184 MUTATED"        
D129V2, continuous
                  vv
clus               STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ZNF184 MUTATED          0         0         4         0        0
  ZNF184 WILD-TYPE        2         6        19         1        1
D129V3, multiclass
           clus
vv          ZNF184 MUTATED ZNF184 WILD-TYPE
  STAGE IB               0                2
  STAGE IIA              0                6
  STAGE IIB              4               19
  STAGE III              0                1
  STAGE IV               0                1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T2+T3+T4
  ZNF184 MUTATED          4
  ZNF184 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D129V5, binary
                  cls
clus                0  1
  ZNF184 MUTATED    0  4
  ZNF184 WILD-TYPE  7 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF184 MUTATED      0    4
  ZNF184 WILD-TYPE    7   21
   clus
vv  ZNF184 MUTATED ZNF184 WILD-TYPE
  0              0                7
  1              4               21
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  ZNF184 MUTATED    2  0  2
  ZNF184 WILD-TYPE 17  1 11
D129V6, multiclass
    clus
vv   ZNF184 MUTATED ZNF184 WILD-TYPE
  M0              2               17
  M1              0                1
  MX              2               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V7, binary
                  cls
clus                0  1
  ZNF184 MUTATED    2  2
  ZNF184 WILD-TYPE 12 17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF184 MUTATED      2    2
  ZNF184 WILD-TYPE   12   17
        clus
vv       ZNF184 MUTATED ZNF184 WILD-TYPE
  FEMALE              2               12
  MALE                2               17
[1] 2 2
[1] FALSE
                  vv
clus               PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ZNF184 MUTATED                                     4
  ZNF184 WILD-TYPE                                  24
                  vv
clus               PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ZNF184 MUTATED                                       0
  ZNF184 WILD-TYPE                                     3
                  vv
clus               PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ZNF184 MUTATED                                                  0
  ZNF184 WILD-TYPE                                                2
D129V8, multiclass
                                                  clus
vv                                                 ZNF184 MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                         0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA              0
                                                  clus
vv                                                 ZNF184 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V9, continuous
[1] "Remove cluster labels:" "ZNF184 MUTATED"        
clus
  ZNF184 MUTATED ZNF184 WILD-TYPE 
               2                9 
      TCGA-FB-A5VM       TCGA-FB-A78T       TCGA-FB-A7DR       TCGA-H8-A6C1 
"ZNF184 WILD-TYPE" "ZNF184 WILD-TYPE" "ZNF184 WILD-TYPE" "ZNF184 WILD-TYPE" 
      TCGA-IB-7885       TCGA-IB-8126       TCGA-IB-A5SS       TCGA-LB-A7SX 
"ZNF184 WILD-TYPE" "ZNF184 WILD-TYPE" "ZNF184 WILD-TYPE" "ZNF184 WILD-TYPE" 
      TCGA-OE-A75W 
"ZNF184 WILD-TYPE" 
D129V10, binary
                  cls
clus                0  1
  ZNF184 MUTATED    2  2
  ZNF184 WILD-TYPE 22  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF184 MUTATED      2    2
  ZNF184 WILD-TYPE   22    7
    clus
vv   ZNF184 MUTATED ZNF184 WILD-TYPE
  R0              2               22
  R1              2                7
[1] 2 2
[1] FALSE
D129V11, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF184 MUTATED       0                         0     4
  ZNF184 WILD-TYPE     2                         3    24
D129V12, multiclass
                           clus
vv                          ZNF184 MUTATED ZNF184 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                3
  WHITE                                  4               24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(130) Variable = ANK3 MUTATION ANALYSIS
D130V1, survival
                sevent
clus2             0  1
  ANK3 MUTATED    2  1
  ANK3 WILD-TYPE 16  4
  ANK3 MUTATED ANK3 WILD-TYPE 
             3             20 
  ANK3 MUTATED ANK3 WILD-TYPE 
             1              4 
$`ANK3 MUTATED`
TCGA-FB-A7DR TCGA-IB-7651 TCGA-IB-7885 
         166         1989          851 

$`ANK3 WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7918 
         360          153          449            1          396           28 
TCGA-HZ-7925 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-8126 TCGA-IB-A5SO 
         361           11           13          476           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         300         1991            8         1968          127          110 
TCGA-Q3-A5QY TCGA-US-A776 
         416          844 

  ANK3 MUTATED ANK3 WILD-TYPE 
           166              1 
  ANK3 MUTATED ANK3 WILD-TYPE 
          1989           1991 
  ANK3 MUTATED ANK3 WILD-TYPE 
         851.0          314.5 
[1] "166.0 - 1989.0 (851.0)" "1.0 - 1991.0 (314.5)"  
[1] "hr=" "1.3"
D130V2, continuous
                vv
clus             STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  ANK3 MUTATED          0         1         2         0        1
  ANK3 WILD-TYPE        2         5        21         1        0
D130V3, multiclass
           clus
vv          ANK3 MUTATED ANK3 WILD-TYPE
  STAGE IB             0              2
  STAGE IIA            1              5
  STAGE IIB            2             21
  STAGE III            0              1
  STAGE IV             1              0
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T2+T3+T4
  ANK3 MUTATED          4
  ANK3 WILD-TYPE       29
[1] "NOT AVAILABLE: table dimension [2x1]"
D130V5, binary
                cls
clus              0  1
  ANK3 MUTATED    0  3
  ANK3 WILD-TYPE  7 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED      0    3
  ANK3 WILD-TYPE    7   22
   clus
vv  ANK3 MUTATED ANK3 WILD-TYPE
  0            0              7
  1            3             22
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  ANK3 MUTATED    3  1  0
  ANK3 WILD-TYPE 16  0 13
D130V6, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  M0            3             16
  M1            1              0
  MX            0             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V7, binary
                cls
clus              0  1
  ANK3 MUTATED    2  2
  ANK3 WILD-TYPE 12 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED      2    2
  ANK3 WILD-TYPE   12   17
        clus
vv       ANK3 MUTATED ANK3 WILD-TYPE
  FEMALE            2             12
  MALE              2             17
[1] 2 2
[1] FALSE
                vv
clus             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  ANK3 MUTATED                                     3
  ANK3 WILD-TYPE                                  25
                vv
clus             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  ANK3 MUTATED                                       0
  ANK3 WILD-TYPE                                     3
                vv
clus             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  ANK3 MUTATED                                                  1
  ANK3 WILD-TYPE                                                1
D130V8, multiclass
                                                  clus
vv                                                 ANK3 MUTATED ANK3 WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                         3             25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                       0              3
  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"
D130V9, continuous
D130V10, binary
                cls
clus              0  1
  ANK3 MUTATED    4  0
  ANK3 WILD-TYPE 20  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED      4    0
  ANK3 WILD-TYPE   20    9
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  R0            4             20
  R1            0              9
[1] 2 2
[1] FALSE
D130V11, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ANK3 MUTATED       1                         0     3
  ANK3 WILD-TYPE     1                         3    25
D130V12, multiclass
                           clus
vv                          ANK3 MUTATED ANK3 WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              3
  WHITE                                3             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
